| Resolved |
Date |
First Name |
Last Name |
Email |
Institution |
Subject |
Webpage |
Comments |
| no |
2013-05-22 08:02:47 |
Moreno |
Colaiacovo |
moreno.colaiacovo@entecra.it |
Agricultural Research Council - Italy |
Bug report |
http://www.plexdb.org/modules/tools/datamine/fluctuation_filter_result_v2.php?array_and_acc_nos=Array&array=ATH1-121501&user_acc_nos=AT4&method=RMA&comparison_operator=%3C&user_cv=10&user_max_limit=1000000 |
Hi
I want to inform you about an issue that I found using the PLEXdb Fluctuation Tool. While performing some analyses with Arabidopsis, I noticed that some experiments have the CVs in a different format, i.e. e.g. 0.20 instead of 20.
For example, check experiment AT4: EVERY probeset in this experiment has CV<1. That's quite strange! In fact, by inspecting the expression profiles, you can see that some probesets show large variations. Probably the CV values were not converted to the percentage! This is a problem, because if you filter experiments to keep only probesets with a CV less than 10, the tool keeps ALL the probesets (instead it should keep only those with a CV less than 0.10).
Hope this will help you.
Best regards,
Moreno |
| no |
2013-03-08 21:53:25 |
Hao |
Wang |
wanghao@uga.edu |
University of Georgia |
Question |
http://www.plexdb.org/modules//Your_Account/index.php?op=mail_done |
Hi,
My current project need to know tissue and developmental expression pattern of some grass genes. I now have fasta sequences of these genes. Could you give instructions on how to perform this kind of analysis in PLEXdb?
Many thanks |
| no |
2013-03-08 21:52:49 |
Hao |
Wang |
wanghao@uga.edu |
University of Georgia |
Question |
http://www.plexdb.org/modules//Your_Account/index.php?op=mail_done |
Hi,
My current project need to know tissue and developmental expression pattern of some grass genes. I now have fasta sequences of these genes. Could you give instructions on how to perform this kind of analysis in PLEXdb?
Many thanks |
| no |
2013-03-04 11:49:44 |
Kevin |
Murray |
kevin.murray@jacks.sdstate.edu |
South Dakota State University |
Question |
http://www.plexdb.org/modules/PD_browse/experiment_browser.php? |
Is there a method to retrieve the numerical expression data for only the specific probesets that are searched? For example in Experiment PT2 of PoplarPLEX Experiment Data I searched 15 probesets, all of which are displayed on a graph. Is there a way that I can retrieve those data points from a download rather than manually recording them? |
| no |
2013-02-07 14:00:27 |
Benjamin |
Benson |
bvbenson@jacks.sdstate.edu |
South Dakota State University |
Question |
http://www.plexdb.org/modules/PD_general/feedbackcgi.php? |
I am interested in downloading the probe set id\'s attached to the nucleotide sequences(example >244901_at:594:703\r\nTTGCTGCTATTCTATCTATTTGTGC) for several of they plant species available on your webpage, but I am having trouble tracking them down except the set of data for Arabidopsis. I was wondering if you have a listing of these on your site, or if you could help me to navigate to them through the links on your page. \r\n\r\nthank you |
| no |
2013-01-26 01:23:57 |
Fariba |
Rafiei |
fariba.rafiei@gmail.com |
shahrekord university |
Question |
http://www.plexdb.org/modules/PD_general/feedbackcgi.php? |
Dear colleague\r\nGreetings!\r\nFirst of all, I would like to appreciate you for the wonderful and informative website you designed. Secondly, I have a technical question regarding probe sets in your web site. I am working on Medicago truncatula, and I was looking for annotation for some of co over expressed probe sets in Plexdb. Luckily, I could reach them in Gene List Suit but when I clicked on the probe set name, a new page was opened and there was a sequence more than 300 bp long in button of the page. It is not probe set because the probe sets are very short. I am wondering if they are EST of M truncatula or any other type of transcriptome of M. truncatula. I would appreciate you if you can help me about the question.\r\n \r\nSincerely yours\r\nFariba Rafiei |
| no |
2012-11-30 09:39:25 |
Frances |
Trail |
trail@msu.edu |
Michigan State University |
Head of lab missing |
http://www.plexdb.org/index.php? |
Hello, Heather Hallen in my lab submitted several experiments using the Fusarium GeneChip. I am not listed as Head of Lab on your PLEX Express links from the MIPS website. Heather is no longer in my lab and her email associated with this work is defunct. I would like my name, at least, to be present so if folks have questions they know who to contact.
thanks very much. |
| no |
2012-08-15 14:03:08 |
Mark |
Voorhies |
mark.voorhies@ucsf.edu |
University of California, San Francisco |
Dead link |
http://www.plexdb.org/modules/PD_browse/queryExperimentsResults.php? |
I'm looking for a data set of four strains of Fusarium graminearum grown for 48 hours on complete media.
This data set is cited as NF3 in the methods section (microarray data analysis) of PLoS Pathogens 8:e1002724 (http://www.ncbi.nlm.nih.gov/pubmed/22693448), but the NF3 data set in PlexDB is from a different paper (a co-infection with Fusarium and Ustilago maydis).
The other two data sets from PLoS Pathogens 8:e1002724 *are* available in PlexDB as FG18 and NF1 (cited in the paper as NF2).
Is the complete media data set available (and, if so, can you point me to the correct accession)?
Thank you for your time,
Mark |
| no |
2012-07-18 10:25:17 |
Betty |
Hosseinpour |
bhosseinpour@gmail.com |
IROST |
Question |
http://www.plexdb.org/modules/PD_probeset/annotation.php?array_name=Wheat&sequence_id=Ta.10069.1.S1_at |
Dear Sir or Madam,
I need to find all probsets related to expansin genes in wheat. But I can't do that in Plexdb. Could you help me to solve my problem.
Thanks
Betty |
| no |
2012-07-16 05:38:02 |
Pablo |
Carbonell-Bejerano |
pablo.carbonell@icvv.es |
Instituto de las Ciencias de la Vid y el Vino (ICVV-CSIC) |
Question |
http://www.plexdb.org/modules/PD_browse/popup_experiment_desc.php?experiment_id=1611 |
Dear PlexDB team,
I uploaded experiment VV33 in PlexDB. The data have been already published and I want to release public access to VV33 and indicate on it the publication reference. How could I edit VV33 experiment? |
| no |
2012-07-16 03:17:53 |
Justin |
Lashbrooke |
jglash@sun.ac.za |
Weizmann Institute of Science |
Question |
http://www.plexdb.org/modules/PD_general/searchcgi.php?search_type=experiment&q=vv33&name=PD_general&page=searchcgi.php |
Hi,
I am looking for experiment VV33. It is referred to in a recent paper in PLOS One. (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039547#s4)
According to the paper the data from the microarrays performed in the work have been deposited at PLEXdb under VV33.
Thanks for your help,
Justin |
| no |
2012-05-25 11:21:40 |
Sudhansu |
Dash |
sdash.sdash@yahoo.com |
ISU-PLEXdb |
test-2 by curator from production |
http://www.plexdb.org/index.php? |
test-2 by curator from production |
| no |
2012-05-13 09:55:44 |
Eve |
Wurtele |
mash@iastate.edu |
ISU |
wow! |
http://www.plexdb.org/modules/PD_general/personnel.php? |
I hadn't tried Plex for quite a while, and just used it to download soybean laser capture data. It is really nice, easy to use lots if functionalities! Great design. thank you, developers! |
| no |
2012-05-09 10:27:39 |
Dan |
Auld |
daniel.auld@thonsomreuters.com |
Thomson Reuters |
Collaboration |
http://www.plexdb.org/index.php? |
Collaboration on Data Citation
Dear Sir/Madam
I am contacting you to enquire if Plexdb would be willing to collaborate with Thomson Reuters on a project to investigate the best ways to support discovery, access, citation, and attribution of digital resources. Initially this will focus on the data sets deposited in repositories, which are used in the research published in the traditional scientific literature.
We would like to:
• Create categorised description records of data sets to aid discovery
• Link the data set description record to the published literature which has used them and which are indexed in our traditional bibliographic databases such as Web of Science®, BIOSIS Citation Index etc.
• Link the data set description record to the data deposited in the repository
• Encourage citation of data by providing attribution and measurement of citation in the traditional literature
We have been working with an expanding number of international data repositories, including ICPSR, Australian Social Sciences Data Archive, UK Data Archive, Pangaea, CanGEM, Refold, Gene Expression Omnibus. We would very much like to work with you to include records for data sets deposited in Plexdb.
Many repositories provide an open access metadata feed, usually in XML which we have been able to use as a basis to create a bibliographic style record, and link back to the repository as the “publisher” of the data. Others have provided a bespoke XML feed for us.
The provision of repository metadata would enable us to link users of our Web of Knowledge platform to the data sets deposited in the repository and demonstrate the value of the data through analysis of citations in the published literature. At no point would we use or store the data sets themselves.
If you feel that collaboration would be possible, we would be happy to discuss the best way to obtain a metadata feed and explain more about the project on the telephone.
Thank you for your time. We look forward to hearing from you.
Regards,
Dan Auld |
| no |
2012-03-29 02:40:30 |
Salvatore |
Camiolo |
s.camiolo@uniss.it |
Università di Sassari |
Question |
http://www.plexdb.org/modules/tools/plexdb_blastresults.php? |
Dear Curators,
first of all thank you very much for the incredible work you are doing with the PLEXdb. It represents a terrific resource for my everyday work. I have a problem that I hope you can help me with. I usually work on correlatiing the expression and the gene structure. However I found very hard to find a correspondence between the Affymetrix probe id and the phytozome annotation of genes. Can you provide me this kind of information?
thanks a lot for your help
Best regards
Salvo |
| no |
2012-01-29 06:36:38 |
Matthew |
Studham |
matthew.studham@gmail.com |
Iowa State University |
Question |
http://www.plexdb.org/modules/submission/index.php? |
I am planning on submitting experiment data but I do not have EXP files. I do have a CEL file for each GeneChip and detailed experiment data (including hybridization info). The ISU GeneChip Facility performed the hybridizations. Do you know if there is a way I can create these EXP files now? |
| no |
2011-12-26 13:13:04 |
Betty |
Hosseinpour |
bhosseinpour@gmail.com |
IROST |
Data error |
http://www.plexdb.org/modules/glSuite/gl_main.php? |
Hi
thank you for your good site! I need to extract the probe set IDs of wheat expansin genes. I went to Gene list suite but it gave me error. Can you help me to do this job?
Best
Betty |
| no |
2011-12-14 15:08:30 |
Eric |
Johnson |
eric.johnson2@ars.usda.gov |
USDA-ARS |
Question |
http://www.plexdb.org/modules/PD_browse/popup_sample_info.php?experiment_id=1162&sample_id=3798 |
in the classic expression graph, the "y-axis" is the log intensity. Is this the log2 intensity? Or something else?
Thank you
Eric |
| no |
2011-12-09 09:31:50 |
Harold |
Kistler |
hckist@umn.edu |
USDA |
Question |
http://www.plexdb.org/modules/PD_general/pathogens_list.php? |
Hi. We are trying to submit the first experiments using the Nine fungal affymetrix array. It is not currently listed on the drop-down box of the submission page. Can you please tell us how to proceed? |
| no |
2011-12-03 00:28:33 |
sweta |
mohan |
swetabiotech88@gmail.com |
IARI, India |
gene expression |
http://www.plexdb.org/modules/PD_probeset/annotation.php?genechip=maize18k&exemplar=Zm.7570.1.A1_at |
its a good database. v useful. |
| no |
2011-11-30 12:20:14 |
Lewis |
Bowman |
lbowman@mailbox.sc.edu |
Universit of South Carolina |
Question |
http://www.plexdb.org/modules/PD_probeset/batch_annotation.php? |
I am trying to download annotations for Maize 58k NSF array. The annotations are displayed but the names of the probesets is blank. Since there area several listings for each probeset, it is impossible to determine which annotations belong to which probesets. Thanks |
| no |
2011-11-17 14:52:13 |
Grant |
Cramer |
cramer@unr.edu |
UNR |
Dead link |
http://www.plexdb.org/modules/PD_probeset/annotation.php? |
Your blasts on the grape annotation page are way out of date, UniProt has a new set IDs and the current links are dead. Can you update these? |
| no |
2011-10-13 16:00:02 |
Eric |
Johnson |
eric.johnson2@ars.usda.gov |
USDA ARS |
Question |
http://www.plexdb.org/modules/submission/learn_plex_express.php? |
I am interested in seeing a GEO accession getting placed into the PLEXdb. I have found the CEL files on the GEO website, but I have not found the EXP files.
The GEO accession is not my own data, but it would be very interesting to have it placed into PLEXdb for my own research.
I welcome your suggestions. Thank you
Eric |
| no |
2011-10-06 09:28:36 |
Birgit |
Samans |
Birgit.Samans@agrar.uni-giessen.de |
University |
|
http://www.plexdb.org/modules/PD_general/personnel.php? |
Dear PlexDB-Team,
we would like to submit an experiment to PlexDB. This experiment is also already available at the ArrayExpress platform. Is there an easy way to transfer the data?
Best regards
Birgit Samans |
| no |
2011-10-01 10:41:46 |
Mariana |
Mondragon Palomino |
m.mondragonpalomino@gmail.com |
University of Regensburg |
Dead link |
http://www.plexdb.org/modules//glSuite/gl_main.php? |
Hello,
I have been trying to obtain a list of genes from specific treatments from the experiment ZM37: genome-wide atlas expression of maize. For this I used the Gene List Suite by specifying the following options:
-Method : Treatment-specific expressed genes
-Array design: Nimblegen Maize Whole-Genome Microarray 385 (Version V2_5a.59)
-Experiment to fetch my list of genes: ZM37: Genome wide gene expression atlas of maize inbred line B73
In the list of organism parts I chose to list all genes expressed in immature cob or other tissues, but regardless of the option I take, I get an error message that shows my search options in the query language for the database, but no data. Just to test the problem was not on my browser, I followed the same procedure with an array in Arabidopsis thaliana and was able to perform my query as I wanted in Z. mays.
I look forwards to your answer and appreciate you look into this question. |
| no |
2011-07-27 11:21:25 |
Rohan |
Patel |
rohan.patel@utoronto.ca |
University of Toronto |
Scripts request |
http://www.plexdb.org/about_plexdb.php? |
Dear Sir/Madam,
I wanted to obtain the Normalization scripts for Experiment ZM29 in Maize "Genome-wide gene expression atlas of maize inbred line B73". On GEO, it says I can obtain these scripts from the PlexDB team.
Would it be possible for you to send this to me at rohan.patel@utoronto.ca?
I look forward to your reply.
Sincerely,
Rohan Patel |
| no |
2011-05-12 10:43:43 |
Gilles |
Jonker |
g.jonker@elsevier.com |
Elsevier |
Suggestion |
http://plexdb.org/index.php? |
We are very pleased to inform you that the second Current Opinion conference will focus on Plant Genome Evolution. The meeting will be chaired by Dr. Yves van de Peer and will take place from 4-6 September 2011 in NH Grand Krasnapolsky, Amsterdam, The Netherlands. For more information please visit www.plantgenomeevolution.com
Dr. van de Peer suggested that we would contact your organisation and that we inform your members about the conference. Given the abstract submission deadline of the 23rd of May it would have our preference to contact your members on short notice. Would this be possible?
Some of the advertisement options that we would be interested to explore are:
• Sending an e-mail message to your members (one-time use of the addresses)
• Banner at your website
• News item in your Newsletter
• RSS feeds, etc.
I have ranked the options in order of our preference. I would be interested to hear whether we can collaborate and what advertisement options would work best from your perspective.
Please contact me in case you have any questions or need further information.
Best Regards,
Gilles
Gilles Jonker
Executive Publisher | Agriculture, Plant and Soil Sciences | Elsevier
Radarweg 29, 1043 NX Amsterdam, The Netherlands
Tel: +31 20 485 2780 |
| no |
2011-05-09 06:51:18 |
CATERINA |
MARE |
caterina.mare@entecra.it |
Genomics Research Centre |
Question |
http://www.plexdb.org/modules//glSuite/gl_main.php? |
Hello, I'm working on grape microarray, I would like to know if is possible how and where to download the additional annotation by cramer el al. in grape array.
Thank you
cordially
Caterina Marè |
| no |
2011-05-04 19:08:54 |
Ann |
Loraine |
aloraine@uncc.edu |
UNC Charlotte |
Suggestion |
http://www.plexdb.org/index.php? |
Hello,
I would like to recommend adding this data set to PLEX:
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5628
AtGenExpress: Stress Treatments (Heat stress)
Thank you!
Ann Loraine |
| no |
2011-03-02 17:31:06 |
Roger |
Wise |
rpwise@iastate.edu |
ISU |
Dead link |
http://www.plexdb.org/modules/PD_probeset/annotation.php?genechip=Maize100WT |
On maize 100WT annotation,
Brachy alignment gives the following message: Server not found
Firefox can't find the server at www.brachypodium.orgcgi-bin. |
| no |
2011-02-10 10:58:15 |
Roger |
Wise |
rpwise@iastate.edu |
USDA-ARS |
Question |
http://www.plexdb.org/modules/glSuite/gl_main.php? |
Annotation tool in GeneList suite is different than annotation under "Tools"
This is still confusing users |
| no |
2011-02-10 10:08:12 |
Roger |
Wise |
rpwise@iastate.edu |
USDA-ARS |
Data error |
http://www.plexdb.org/modules/PD_browse/profileneighbors_download.php?accession_no=BB2&method=mas&probeset=Contig3197_at&probesetsonly=yes&exporttype=export |
Profile Neighbors - Only get 1 ID in the list even though 29 lines show up on graph; please fix this bug:
Generated by PLEXdb on Feb-10-2011
Profile neighbor data for probe set Contig3197_at in BB2
Probe_Set_ID
Contig3197_at |
| no |
2011-02-09 15:57:48 |
Greg |
Fuerst |
gsfuerst@iastate.edu |
USDA-ARS |
Suggestion |
http://www.plexdb.org/404.php? |
During experiment submission;
To optimize experiment submission, you should have the option of re-ordering Factor levels,as well as Factors
Thanks |
| no |
2011-02-01 14:58:17 |
Gregory |
Hazen |
ghazen@iastate.edu |
ISU |
Question |
http://www.plexdb.org/modules/PD_general/feedbackcgi.php? |
Does a publicly available API exist for accessing data from PLEXdb using programing? If so, where can I find documentation? |
| no |
2011-01-26 13:22:34 |
Mary |
Schaeffer |
schaefferm@missouri.edu |
USDA |
Suggestion |
http://www.plexdb.org/modules/PD_browse/experiment_browser.php?experiment=ZM29 |
In the text for this one 'expriment' needs to be experiment (only one time) |
| no |
2011-01-24 10:35:34 |
Ann |
Loraine |
aloraine@uncc.edu |
UNCC |
Suggestion |
http://www.plexdb.org/index.php? |
Hi,
I'm writing to request importing of GSE accession GSE12404 into PLEXdb, titled "Expression data from Arabidopsis Seed Compartments at 5 discrete stages of development."
Thanks you so much and please let me know if you have any questions about it!
Very best wishes,
Ann Loraine |
| no |
2011-01-19 18:15:56 |
Roger |
Wise |
rpwise@iastate.edu |
ISU |
Suggestion |
http://www.plexdb.org/modules/PD_general/feedbackcgi.php? |
http://www.plexdb.org/modules/PD_general/Maize100WT_description.php#S1\r\n\r\nRemove \ |
| no |
2011-01-19 13:06:03 |
Sen |
Subramanian |
manianslab@gmail.com |
South Dakota State University |
Question |
http://www.plexdb.org/modules/PD_general/feedbackcgi.php? |
Can we submit expression data from high throughput sequencing (RNAseq) experiments to plexDB?\\r\\n\\r\\nThanks,\\r\\nSen |
| no |
2011-01-18 08:52:47 |
Justin |
Lashbrooke |
jglash@sun.ac.za |
Institute for Wine Biotechnology |
Question |
http://www.plexdb.org/modules/glSuite/gl_main.php? |
When will the Co-expression function for tomato genes be functional? And will you be uploading any Nimblegen Array data? |
| yes |
2011-01-12 23:47:02 |
Neil |
Shirley |
neil.shirley@acpfg.com.au |
University of Adeliade |
Question |
http://www.plexdb.org/modules/tools/plexdb_blast.php? |
What separator is needed between probes when using PLEXDb Blast "probe set IDs"? Comma doesnt work.
Cheers,
Neil |
| yes |
2011-01-07 09:28:09 |
Roger |
Wise |
rpwise@iastate.edu |
ISU |
Bug report |
http://www.plexdb.org/index.php? |
When I selected soybean expression atlas (GM20) I think, no display is presented |
| yes |
2010-12-27 13:57:38 |
Ann |
Loraine |
aloraine@uncc.edu |
UNC Charlotte |
Suggestion |
http://www.plexdb.org/modules/PD_general/personnel.php? |
Hello,
I'm writing to make a special request for a new data set to be added to PLEX.
Could you add this data set?
The GEO accession is GSE680 and the array platform is ATH1 22K.
The experiment is described here:
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE680
and is published in this article:
http://www.ncbi.nlm.nih.gov/pubmed/20385809
Thank you and very best wishes!
Ann Loraine
|
| yes |
2010-12-22 17:26:58 |
Ann |
Loraine |
aloraine@uncc.edu |
UNCC |
Suggestion |
http://www.plexdb.org/index.php? |
Hi!
It would be great if the pull-down menu listing experiments could be wider so that I can read more of the experiment description.
Thank you!
Ann |
| yes |
2010-12-21 19:51:20 |
Roger |
Wise |
rpwise@iastate.edu |
ISU |
Data error |
http://www.plexdb.org/modules/PD_general/publications.php? |
Please fix citation on publications page:
Mar�a Mu�oz-Amatria�n, .............. |
| yes |
2010-12-21 19:29:44 |
Roger |
Wise |
rpwise@iastate.edu |
ISU |
Data error |
http://www.plexdb.org/modules/PD_general/publications.php? |
Please fix citation on publications page:
Mar�a Mu�oz-Amatria�n, .............. |
| yes |
2010-12-21 19:26:53 |
Roger |
Wise |
rpwise@iastate.edu |
ISU |
Suggestion |
http://www.plexdb.org/index.php? |
Default on experiment page should be "Expression" Please make it so |
| yes |
2010-12-13 11:29:21 |
Roger |
Wise |
rpwise@iastate.edu |
Iowa State University |
Suggestion |
http://www.plexdb.org/index.php? |
Default display is pointing to "experiment" not Expression. Please make the default to 'Expression' |
| yes |
2010-11-25 06:28:40 |
Peter |
von Rohr |
peter@nebion.com |
Nebion AG |
Question |
http://www.plexdb.org/index.php? |
Dear PLEXdb-team,
I was wondering whether there is any possibility to download CEL files from your repository using command-line tools such as wget or lynx or ...
Thanks in advance, best regards
Peter von Rohr |
| no |
2010-11-18 10:07:28 |
Ajay |
Prasad |
prasada@student.ethz.ch |
ETH Zurich |
Question |
http://www.plexdb.org/modules/PD_general/feedbackcgi.php? |
I would like to know how is the annotation done using the tool :
"Download annotation for probeset ids".
Actually I am trying to find the annotation for Oryza sativa probesets but from the above mentioned tool, I am getting very low percent identity for more than 10000 sequences. Therefore, I am curious about your gene annotation process.
Since, it is not provided in your documentation, I will be grateful if provided with any information regarding the "annotation for probesets" tool. Thanks. |
| no |
2010-11-08 10:31:13 |
Yvette |
Wilson |
Yvette.Wilson@scri.ac.uk |
University of dundee |
Question |
http://www.plexdb.org/modules/glSuite/gl_main.php? |
Hi
I would like to annotate a list of barley 22K probesets with the nearest Arabidopsis gene. However the annotated table that is output since the last blast (03-11-2010) does not give a description of the gene function (just its chromosome location and length) - which I would find useful. Is there an easy way to get this?
many thanks
Yvette |
| yes |
2010-10-13 03:02:07 |
Imre |
Somssich |
somssich@mpiz-koeln.mpg.de |
Max Planck Institute for Plant Breeding |
Data error |
http://www.plexdb.org/modules/PD_general/feedbackcgi.php? |
Related to our microarray data AT46 (Targets of AtWRKY27 in Arabidopsis leaves Mukhtar S, Somssich I), it is unclear to me why three additioal persons are listed: Townsend H, Emmerson Z, Schildknecht B,? I do not know these persons and they have not been part of our experiment.\\r\\n\\r\\nbest regards,\\r\\n\\r\\nI. E. Somssich
Curator:
These additional names were listed as contributers at NCBI GEO (GSE5537) from which PLEXdb imported your experiment. On your request, I have removed these names from AT46. We appreciates your review of the experiment and the feedback.
|
| yes |
2010-09-01 08:55:14 |
wenkai |
jiang |
biology0046@hotmail.com |
kunming institute of botany |
Question |
http://www.plexdb.org/modules/PD_general/feedbackcgi.php? |
Hi,\r\nI try to use the AT40 expression data in my research,\r\nbut i found that the RMA normalized expression value is different from the data table downloaded from Atgenexpress (http://www.weigelworld.org/resources/microarray/AtGenExpress/AtGE_dev_gcRMA.txt.zip/view)\r\nthe exp value from Atgenexpress is log2 transformed,\r\n\r\nmy question is that does the difference cause by different log base values?\r\nis the RMA value present in Plexdb log2 transformed?\r\n\r\nbest regard!
Curator:
Yes, the RMA normalized expression values are logged to the base 2. We
use the Bioconductor affy package for normalization.
|
| yes |
2010-07-29 08:30:38 |
Simon Peter |
Gough |
simon.gough@biokem.lu.se |
Lund University |
Question |
http://www.plexdb.org/modules/PD_probeset/batch_annotation_results.php? |
Dear Curator
When doing a blast search with a sequence I can find a barley contig and a link which usually shows a Gene Index link(HvGi).
In this way I can find that the Gene of Contig725_s_at is TC168092.
I wish to find the Gene Index acc.no for a set of contigs.
However if I use "Download Annotation for Probesets " and just ask to see "Gene Index ID" , nothing is returned either with a single sequence or a set.
It would be very usefull to correlate Gene Index nos with contig nos for larer dtasets and so I suggest that the link is made.
with best regards and thanks
Simon
Curator:
The HarvEST site could be a good source for this purpose.
http://www.harvest-web.org/
|
| yes |
2010-07-28 09:02:19 |
Greg |
Fuerst |
gsfuerst@iastate.edu |
USDA-ARS |
Data error ? |
http://www.plexdb.org/modules/PD_general/feedbackcgi.php? |
After downloading the "MAS treatment means for all probesets (.txt)" for BB10, we transformed these data to log base 2. We then compared these data against the probeset figure data for our gene of interest, Contig12219_at, and they did not match. Can you please look at this at tell us which data are correct. Also, is this an isolated incident or are others in the BB10 experiment wrong as well.
PLEXdb Curator's Response:
The data is not wrong. The downloaded file containing the treatment means shows un-logged mean of the replicates. On the other hand, the expression plot when it displays the treatment means, shows the mean of individual logged values of the replicates. For further analysis we recommend using the values from the downloaded file. |
| yes |
2010-06-10 01:48:57 |
Graham |
McGrann |
graham.mcgrann@bbsrc.ac.uk |
John Innes Centre |
Suggestion |
http://www.plexdb.org/modules/PD_probeset/annotation.php?genechip=Wheat |
Are there any plans to include a blast analysis of the cereal Affymetrix transcript sequences against the recently released Brachypodium genome sequence? This could be very useful for those study cereal comparative transcriptomics?
PLEXdb Curator:
We will include Brachypodium in PLEXdb in the near future.
|
| yes |
2010-06-03 11:31:10 |
Arnaud |
Bottin |
bottin@scsv.ups-tlse.fr |
Université de Toulouse |
Bug report |
http://www.plexdb.org/modules/Your_Account/index.php?op=new_user |
Dear colleague, I was unable to create my account : I got the message "The errors listed below must be corrected before continuing" apparently because the program was unable to retain the "primary job" I selected in the list
Please let me know if this can be solved
Best regards
Arnaud Bottin |
| yes |
2010-03-16 10:49:43 |
Carla |
Pinheiro |
pinheiro@itqb.unl.pt |
ITQB |
Question |
http://www.plexdb.org/modules/PD_general/publications.php? |
Dear Sirs,
How to cite PLEXdb? Just add the link on the text? I will soon submit a manuscript and am not sure how to procedd. Thank you so much. |
| yes |
2010-03-07 21:20:23 |
Anar |
Khan |
anar.khan@agresearch.co.nz |
AgResearch |
Question |
http://www.plexdb.org/modules/PD_probeset/multi_annotation.php?tmva=0|33|53|63|65|76| |
Hi
PLEXdb looks like a fantastic resource! I am about to start analysing some Affymetrix wheat chip data and I was wondering whether it is possible to obtain the full set of GO annotations, for all probe sets on the chip, as a tab-delimited text file? Also, could you please tell me when the GO annotations were last updated and whether you believe they are superior to the Affymetrix annotations?
Many thanks,
Anar |
| yes |
2010-02-23 10:44:40 |
Jian-Min |
Zhou |
jianmzho@alcor.concordia.ca |
Concordia University |
How to order a DNA (cDNA)clone? |
http://www.plexdb.org/modules/PD_general/news.php? |
How can I order a target gene once I find it in a species?
Thanks. |
| yes |
2010-02-01 16:35:32 |
Jackson |
Moeller |
jacksonr@iastate.edu |
Iowa State University |
[RESOLVED] Question. |
http://www.plexdb.org/modules/PD_general/feedbackcgi.php? |
[RESOLVED].
Hello. I would like my data to also be submitted to GEO, but not yet publicly accessible. Steve Whitham, my major advisor, told me that PlexDB will do this. Can/will you do this for us? Thank you,Jackson |
| yes |
2010-02-01 11:19:12 |
Roger |
Thilmony |
roger.thilmony@ars.usda.gov |
USDA-ARS |
[RESOLVED] Bug report |
http://www.plexdb.org/modules/PD_browse/experiment_browser.php? |
[RESOLVED]
Hi,
I have been trying to visualize individual probe data for Wheat Affy experiments and it works fine for the "expression graph" function for either MAS 5 normalized or RMA normalized data, but when I try switching to "raw probe values" I receive JpGraph errors stating "Empty imput data array specified for plot" even though a functional probeset ID is listed. |
| no |
2010-01-25 16:00:40 |
Taner |
Sen |
taner@iastate.edu |
USDA/ISU |
Bug report [DEFERRED] |
http://www.plexdb.org/modules/PD_general/searchcgi.php?search_type=probeset&q=MZ00011774&name=PD_general&page=searchcgi.php |
[DEFERRED]
I searched for a specific probe from the main page using the dropdown menu , chose "probe", enter MZ00011774, clicked on "GO!". I got the following error message:
Searched for MZ00011774.
Error: Could not connect to the specified database, Affy_Citrus_Annot.Access denied for user 'plexweb'@'%.iastate.edu' to database 'Affy_Citrus_Annot' |
| yes |
2009-12-17 12:43:59 |
Diego |
Lijavetzky |
diegolija@hotmail.com |
CONICET |
Custom Array |
http://www.plexdb.org/modules/submission/experiment_description.php? |
Hi,
I’m beginning an experiment submission and I wonder if is possible to perform “Custom Array” submissions, since this option is not available in the pop-up menu “array design”.
Thank you |
| yes |
2009-12-11 01:59:56 |
Graham |
McGrann |
graham.mcgrann@bbsrc.ac.uk |
John Innes Centre |
Question |
http://www.plexdb.org/modules/Your_Account/downloadlog.php? |
I've recently come across a PlexDB accession in a published paper (TA20 - Transcriptome Analysis of a Wheat Near-Isogenic Line Pair Carrying Fusarium Head Blight-Resistant and -Susceptible Alleles
Jia HY, Cho SH, Muehlbauer GJ
MOLECULAR PLANT-MICROBE INTERACTIONS Volume: 22 Issue: 11 Pages: 1366-1378 Published: NOV 2009) and was wondering if the experiment is going to be made public? |
| NA |
2009-10-13 12:58:58 |
SPAM
TellcledBuilk |
SPAM
TellcledBuilk |
SPAM
|
SPAM
TellcledBuilk |
SPAM
Bug report |
SPAM
|
SPAM
|
| yes |
2009-09-01 01:06:59 |
Jafar |
Jabbari |
jafar.jabbari@uq.edu.au |
DPI&F QLD |
Question |
http://www.plexdb.org/modules/PD_general/feedbackcgi.php? |
To whom it may concern
I wondering how I can download or obtain normalised expression values for all genes on Barley1 22K chip from each hybridisation (treatment and replicates) of a given experiment.
Regards,
Jafar Jabbari |
| yes |
2009-07-16 08:02:20 |
elsa |
ballini |
eballini@iastate.edu |
USDA |
Suggestion |
http://www.plexdb.org/modules/PD_probeset/show_probealign.php?array_name=Barley1&ProbeImageWidth=820&sequence_id=Barley1_01637 |
Hi,
I'd like to have a list of all allelic probeset in the Affymetrix barley array. With this tool I can check for one sequence the name of the allelic probesets but I need to check 5000 probesets and it's too much mannually. So do you have a table with the information for all the probesets? |
| yes |
2009-07-09 04:01:46 |
Endre |
Sebestyen |
endre.sebestyen@gmail.com |
ARI-HAS |
Bug report |
http://www.plexdb.org/modules/PD_probeset/GO_annotation.php? |
Hi!
When I try to use the GO annotation tool for the maize 58k array with the default settings, I only get this error:
Error: Query "SELECT * FROM LIMIT 1" failed to execute You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'LIMIT 1' at line 1
It seems there are some bugs in the SQL query.
Regards,
Endre |
| no |
2009-07-02 09:07:51 |
gjpteeb |
gjpteeb |
lzjacc@zzmudx.com |
PkyoLfujyhHdSNRG |
Bug report |
97 |
T7vCwR hobkfzqmeekr, [url=http://icjguocgsrcd.com/]icjguocgsrcd[/url], [link=http://kfqxsuyyesgm.com/]kfqxsuyyesgm[/link], http://oolphfiinnxu.com/ |
| no |
2009-07-01 17:28:24 |
upendra kumar |
devisetty |
upendra_35@yahoo.com |
UNIVERSITY OF NOTTINGHAM |
|
http://www.plexdb.org/modules/PD_general/feedbackcgi.php? |
Dear curator i would like to know how i can access the experiment which is in GEO (Accession: GSE6027) in Plexdb. Thanks in advance |
| no |
2009-07-01 17:28:08 |
upendra kumar |
devisetty |
upendra_35@yahoo.com |
UNIVERSITY OF NOTTINGHAM |
|
http://www.plexdb.org/modules/PD_general/feedbackcgi.php? |
Dear curator i would like to know how i can access the experiment which is in GEO (Accession: GSE6027) in Plexdb. Thanks in advance |
| no |
2009-06-26 23:30:14 |
Harkamal |
Walia |
hwalia@ucdavis.edu |
UC Davis |
|
http://www.plexdb.org/modules/PD_general/feedbackcgi.php? |
Was wondering when you will make the TA23 experiment available. The paper is published now in BMC Genomics:\\r\\n\\r\\nBMC Genomics. 2009 Jun 24;10(1):279\\r\\n\\r\\nThanks |
| no |
2009-06-26 23:29:59 |
Harkamal |
Walia |
hwalia@ucdavis.edu |
UC Davis |
|
http://www.plexdb.org/modules/PD_general/feedbackcgi.php? |
Was wondering when you will make the TA23 experiment available. The paper is published now in BMC Genomics:\r\n\r\nBMC Genomics. 2009 Jun 24;10(1):279\r\n\r\nThanks |
| no |
2009-06-26 23:29:43 |
Harkamal |
Walia |
hwalia@ucdavis.edu |
UC Davis |
|
http://www.plexdb.org/modules/PD_browse/experiment_browser.php?plex_name=WheatPLEX |
Was wondering when you will make the TA23 experiment available. The paper is published now in BMC Genomics:
BMC Genomics. 2009 Jun 24;10(1):279
Thanks |
| no |
2009-06-10 05:19:56 |
qphyysedb |
qphyysedb |
bklxkl@cvwzil.com |
kCQEukLZcDmve |
Suggestion |
76 |
6C6DiC vmnhmefuvmns, [url=http://rzojjuocdfek.com/]rzojjuocdfek[/url], [link=http://lghcpcrpcbsi.com/]lghcpcrpcbsi[/link], http://vsevqnuyngrh.com/ |
| no |
2009-05-15 00:44:04 |
jktnxinty |
jktnxinty |
ethacw@kkweag.com |
euZCxQVIwtJIWu |
Data error |
70 |
vvjJFa ajbzztmbvhvt, [url=http://phoacnjizdqz.com/]phoacnjizdqz[/url], [link=http://dqcasckuobkw.com/]dqcasckuobkw[/link], http://bpnfslliwzpn.com/ |
| no |
2009-05-15 00:42:54 |
kazddanx |
kazddanx |
uxoiib@qwhlxp.com |
xCbIalAIeFMRZS |
Bug report |
13 |
V7bLVH dvmlsnxknmjm, [url=http://oemxcclvuatu.com/]oemxcclvuatu[/url], [link=http://pbjqjvsygxxb.com/]pbjqjvsygxxb[/link], http://nadomshbwcrh.com/ |
| no |
2009-05-15 00:42:05 |
aivsen |
aivsen |
bpvcuc@wirpvt.com |
CjhQRQGVJsniVpmbkME |
Data error |
37 |
peemQG ekvhjasdslyw, [url=http://hblyejwmkybd.com/]hblyejwmkybd[/url], [link=http://qccfycwazbes.com/]qccfycwazbes[/link], http://saazdxqnhrbr.com/ |
| no |
2009-05-07 23:46:13 |
Livia |
Tommasini |
liviat@uci.edu |
University of California Riverside |
Question |
http://www.plexdb.org/modules/PD_general/feedbackcgi.php? |
Hi! could you please send my password to my new address liviat@uci.edu? Cheers, Livia |
| no |
2009-05-07 23:45:58 |
Livia |
Tommasini |
liviat@uci.edu |
University of California Riverside |
Question |
http://www.plexdb.org/modules/PD_general/feedbackcgi.php? |
Hi! could you please send my password to my new address liviat@uci.edu? Cheers, Livia |
| no |
2009-05-07 23:45:38 |
Livia |
Tommasini |
liviat@uci.edu |
University of California Irvine |
Question |
http://www.plexdb.org/modules//Your_Account/index.php?op=mail_done |
Hi! could you please send my password to my new address liviat@uci.edu? Cheers, Livia |
| no |
2009-04-16 15:06:26 |
livia |
tommasini |
tlivia@yahoo.com |
uci |
Question |
http://www.plexdb.org/modules/PD_general/feedbackcgi.php? |
Hi! I would like to know how long it takes for you to upload data that have been uploaded to PlexDB into GEO. Looking forward to hearing from you. |
| no |
2009-04-16 15:06:00 |
livia |
tommasini |
tlivia@yahoo.com |
uci |
Question |
http://www.plexdb.org/modules/PD_general/feedbackcgi.php? |
Hi! I would like to know how long it takes for you to upload data that have been uploaded to PlexDB into GEO. Looking forward to hearing from you. |
| no |
2009-04-16 15:04:54 |
livia |
tommasini |
tlivia@yahoo.com |
uci |
Question |
http://www.plexdb.org/modules/PD_general/feedbackcgi.php? |
Hi! I would like to know how long it takes for you to upload data that have been uploaded to PlexDB into GEO. Looking forward to hearing from you. |
| no |
2009-04-16 15:04:28 |
livia |
tommasini |
tlivia@yahoo.com |
uci |
Question |
http://www.plexdb.org/modules/PD_general/feedbackcgi.php? |
Hi! I would like to know how long it takes for you to upload data that have been uploaded to PlexDB into GEO. Looking forward to hearing from you. |
| no |
2009-04-16 15:04:04 |
livia |
tommasini |
tlivia@yahoo.com |
uci |
Question |
http://www.plexdb.org/modules/PD_general/feedbackcgi.php? |
Hi! I would like to know how long it takes for you to upload data that have been uploaded to PlexDB into GEO. Looking forward to hearing from you. |
| no |
2009-04-16 15:03:44 |
livia |
tommasini |
tlivia@yahoo.com |
uci |
Question |
http://www.plexdb.org/index.php? |
Hi! I would like to know how long it takes for you to upload data that have been uploaded to PlexDB into GEO. Looking forward to hearing from you. |
| no |
2009-04-13 16:26:46 |
dmoevk |
dmoevk |
nvnvez@nkclsy.com |
KtOrimNyzeUY |
Bug report |
12 |
rfy8YK ktlrcmwzcmvm, [url=http://beugjnjwtehc.com/]beugjnjwtehc[/url], [link=http://ooztvxvysgln.com/]ooztvxvysgln[/link], http://kunevmecfguq.com/ |
| no |
2009-04-13 16:24:47 |
hyangv |
hyangv |
juygnh@hqymbh.com |
CJKDCZvhoPs |
Bug report |
45 |
okhXle zhusuqyxsgtb, [url=http://zqfitintguzk.com/]zqfitintguzk[/url], [link=http://lgjhguijeqju.com/]lgjhguijeqju[/link], http://koilfylvehmc.com/ |
| no |
2009-03-26 22:02:20 |
David |
Young |
young.david1@mayo.edu |
Mayo Clinic |
Suggestion |
http://www.plexdb.org/modules/PD_general/feedbackcgi.php? |
Hello,\r\n\r\n I was reading your explanation of RMA at http://www.plexdb.org/modules/documentation/RMAexplained.pdf and found it very useful. However, on the median polish section, I don\'t really understand where you get the row and column effects at the end. The way I understand it, the column and row effects are swept into a table effect after each iteration (sweeping of rows or columns). This way, the row effect for row 1 would be 4 (or 11 with the table effect added in), as opposed to 12.65. Could you be more explicit about how these last values are obtained? Besides that, it is the best explanation of RMA I\'ve found, so thank you for spending the time to write that up.\r\n\r\nDave |
| no |
2009-03-26 22:02:05 |
David |
Young |
young.david1@mayo.edu |
Mayo Clinic |
Suggestion |
http://www.plexdb.org/index.php? |
Hello,
I was reading your explanation of RMA at http://www.plexdb.org/modules/documentation/RMAexplained.pdf and found it very useful. However, on the median polish section, I don't really understand where you get the row and column effects at the end. The way I understand it, the column and row effects are swept into a table effect after each iteration (sweeping of rows or columns). This way, the row effect for row 1 would be 4 (or 11 with the table effect added in), as opposed to 12.65. Could you be more explicit about how these last values are obtained? Besides that, it is the best explanation of RMA I've found, so thank you for spending the time to write that up.
Dave |
| no |
2009-01-30 05:22:34 |
john |
Whitaker |
bgy1jww@leeds.ac.uk |
University of Leeds |
data download |
http://www.plexdb.org/modules/PD_probeset/show_probealign.php?array_name=ATH1-121501&ProbeImageWidth=820&sequence_id=250434_at |
Hello,
I am trying to obtain the sequences of all the probes on the affy array ATH1. Your site lets me browse the probes for a particular gene; however, I can't find away of downloading the sequences of all the probes. If could obtain a fasta file of the sequences of all the probes in that would be brilliant.
Thanks,
John |
| no |
2009-01-06 19:49:07 |
Roger |
Thilmony |
roger.thilmony@ars.usda.gov |
USDA-Agriculture Research Service |
Question |
http://www.plexdb.org/modules/PD_browse/experiment_browser.php? |
Hi,
I have been using the Browse BarleyBase Experiment Data, "Expression Graph" function to visualize the expression pattern of individual Barley GeneChip probesets in the publicly available datasets.
The function/capability is great and I find it usefull. The graph displaying the expression values across an experimental series is nice. I particularly like the colorfull annotation of the experiments/chip hybs for the X-axis on the bottom of the graph.
Is there a way to download/export this graph with its legend annotation as an image? I can't seem to copy and paste it from the Web browser.
I realize that I can download the data and essentialy build my own graph in excel using the normalized data, but it would certainly be easier if an image could just be exported from PlexDB/BarleyBase.
Thanks,
Roger |
| no |
2008-12-20 17:58:01 |
Grant |
Cramer |
cramer@unr.edu |
University |
Suggestion |
http://www.plexdb.org/modules/PD_general/misc.php? |
It would be nice in the grape annotation section if you linked the probe set to the gene locus in Gramene. Then there would be all kinds of additional annotation such as gene families, proteins, etc. etc. |
| no |
2008-12-19 14:17:11 |
Laurent |
Deluc |
delucl@unr.edu |
UNR |
Bug report |
http://www.plexdb.org/modules/PD_browse/experiment_browser.php? |
Hi, We are in the process to submit a paper and I just double checked that all files of Vv5 experiment are accessible. Unfortunately, readme VV5 MAS RMA.txt and readme VV5 CEL.txt are not readeable. So it would be better if the site was updated before paper is published, so that everything flows
smoothly and looks professional.
Thank you in advance |
| no |
2008-12-03 04:11:00 |
Marek |
Mutwil |
mr_mutwil@interia.pl |
Max-Planck-Gesselshaft |
Question |
http://www.plexdb.org/modules/PD_general/links.php? |
Hi PLEXdb,
I am interested if you could provide me with best BLASTX results for all probesets of Barley1 genechip. I am trying to use blastclust on Arabidopsis and Barley probesets, but it's taking forever.
Kind regards,
Marek Mutwil
|
| no |
2008-10-21 13:08:13 |
Seungho |
Cho |
seungho_cho@hotmail.com |
BASF Plant Science, LLC |
granting access |
http://www.plexdb.org/modules/PD_browse/queryExperimentsResults.php? |
Dear curator,
Dr. Gary Muehlbauer at University of Minnesota needs to create an ID and password for review of the manuscript to access CEL files associated with BB45 and BB47. Please grant right to a reviewer to access these two experiments. It will be OK to create only one ID and password to access these experiment and download if needed. Please inform us as early as possible if this can be done. Thanks a lot. |
| no |
2008-10-20 15:13:39 |
Chunzhen |
Zhang |
chz405@iastate.edu |
Iowa State University |
Question |
http://www.plexdb.org/modules/PD_general/personnel.php? |
I am using The PLECdb now. I wonder if it has a function of clustering the Barley probe (genes) into different function groups? For example, for a group of selected probe IDs, I want to know how many of them are located on cell wall and how many of them related photosynthesis. etc.
If there is no such a function in PLEXdb, can you suggest a website can possibley do this kind of work?
Thanks and Regards,
Chunzhen |
| no |
2008-09-28 14:37:22 |
rivka |
elbaum |
rivka.elbaum@weizmann.ac.il |
Weizmann Institute of Science |
Question |
http://www.plexdb.org/modules/PD_general/feedbackarchive.php? |
Dear Madam or Sir,
what fraction of the barley prob-sets on the Barley1 chip have gene ontologies?
Thank you in advance, Rivka |
| no |
2008-08-18 22:26:38 |
Michael |
Considine |
mickcons@plants.uwa.edu.au |
The University of Western Australia |
Question |
http://www.plexdb.org/modules/PD_probeset/annotation.php?genechip=Grape |
Dear Sir or Madam,
Is it possible to download, or in other way attain a batch or the entire Vitis Affymetrix probe set BLASTX results against the Arabidopsis genome? Preferably including the MIPS annotation?
I have been working on annotating the Vitis Affymetrix to the Arabidopsis genome and believe I may have some improvements to make to your set, but downloading the data individually adds an extra burden to the labourious process already undertaken.
Kind regards, Mick |
| no |
2008-07-19 12:50:26 |
Irina |
Kempel |
irina.kempel@biologie.uni-regensburg.de |
University of Regensburg |
Data error |
http://www.plexdb.org/modules/PD_probeset/batch_annotation.php? |
Hello PLEXdb team!
I tried several times to get annotations with ID from Maize 58k NSF long oligo array, but every time I've got an error. Error: Query "SELECT * FROM annotation.annot_maize57karray WHERE Probe_Set_ID IN ('MZ00000397','MZ00000398','MZ00000399','MZ00000400','MZ00000401')" failed to execute Unknown column 'Probe_Set_ID' in 'where clause'
Could you pleas look at this function?
Thank you in advance. |
| no |
2008-06-19 11:20:54 |
Timothy |
Close |
timothy.close@ucr.edu |
University of California |
|
http://www.plexdb.org/modules/submission/index.php? |
I have been unable to view citrus experiments although I am part of the citrus group. Please advise. |
| no |
2008-06-19 11:18:45 |
Timothy |
Close |
timothy.close@ucr.edu |
University of California |
Barley Links to HarvEST |
http://www.plexdb.org/modules/PD_probeset/annotation.php?genechip=Barley1 |
Please add links to HarvEST:Barley for PlexDB Barley. HarvEST:Barley assembly #25 was the list of exemplars for the Barley1 GeneChip and it provided the original foundation of BarleyBASE. Assembly #25 is a subset of assembly #21, which was more correctly the source of Barley1 GeneChip content. The best annotations of the Barley1 GeneChip are available from HarvEST:Barley using the annotation function within the software. HarvEST:Barley assemblies can be searched by BLAST using http://138.23.191.145/blast/index.html. |
| no |
2008-06-19 10:28:15 |
Mikeal |
Roose |
mikeal.roose@ucr.edu |
University of California |
Suggestion |
http://www.plexdb.org/modules/documentation/FAQs.php? |
It would be helpful if the system allowed group members to review an experiment before it is submitted. I thought that this was going to be possible, but apparently not. The only workaround I can see is to copy the screenshots and send them to the group members. Is this correct? |
| no |
2008-06-16 18:36:56 |
Mikeal |
Roose |
mikeal.roose@ucr.edu |
University of California |
Bug report |
http://www.plexdb.org/modules/submission/protocol_list.php?type=hybridization |
I tried entering a new hybridization protocol and after clicking "Submit" I got an odd error message - something like "invalid protocol type hybrization" (definitely misspelled). I tried a couple more times and now see that 3 version of the same protocol can be edited (but not deleted). Need to fix the submit bug and add a "delete protocol" option. |
| no |
2008-06-12 13:40:12 |
Arjun |
Krishnan |
arjunk@vbi.vt.edu |
Virginia Tech |
Question |
http://www.plexdb.org/modules/PD_probeset/batch_annotation.php? |
Dear Curator,
I wish to obtain annotation for all the probesets in the Maize 18K Affymetrix array mapped onto the Rice genome, but the last option "Get annotation for all probe sets on selected array" does really take a very long time before the browser actually gives up and says that the script is not responding.
Could you kindly provide me with this data: Maize 18K probesets (Zm_xxx.xx.xxx_at) mapped to Rice locus ids (LOC_Osxxgxxxxx)?
Thanks,
Arjun |
| no |
2008-04-22 12:38:58 |
Graham |
McGrann |
graham.mcgrann@bbsrc.ac.uk |
John Innes Centre |
Question |
http://www.plexdb.org/modules/PD_probeset/annotation.php?genechip=Wheat&sequence_id=Ta.11895.1.S1_at |
Is there anywhere on the Plexdb site that outlines how the "find your gene" tools actually works? Does the tool blast the query sequence against the whole of the consensus sequence for an exemplar, or the target sequence for a particular gene or is it just against the probe sequences?
Thanks Graham |
| no |
2008-04-10 10:05:17 |
Greg |
Fuerst |
gsfuerst@iastate.edu |
USDA-ARS |
Bug report |
http://www.plexdb.org/404.php? |
The picture links on the following webpage are broken.
http://www.plexdb.org/modules/submission/learn_plex_treatment.php |
| no |
2008-04-04 07:01:48 |
jan |
svensson |
jsv@life.ku.dk |
University of Copenhagen |
Question |
http://www.plexdb.org/index.php? |
I downloaded a fusarium experiment (FG7) and when I started my data analysis I get an error message (The CEL file may be truncated.) for KYS_8_2_fusariam.CEL. This happens both when I used "affy" in bioconductor and the windows RMAexpress.
Do you know if the CEL file is okay?
Best regards,
Jan
|
| no |
2008-03-22 10:44:51 |
Simon |
Gough |
simon.gough@biokem.lu.se |
Lund |
Suggestion |
http://www.plexdb.org/modules/PD_general/feedbackcgi.php? |
Dear Plex people
It would be very useful if blast was possible using the contig name directly.
best regards and thanks
Simon |
| no |
2008-03-13 02:58:32 |
Simon |
Gough |
simon.gough@biokem.lu.se |
Lund |
Question |
http://www.plexdb.org/modules/PD_browse/experiment_browser.php?section=Downloads&experiment=BB8 |
Could you please make available the text version of the filles for
BB8:Microarray of barley genes in wheat-barley chromosome addition lines Seungho Cho, University of Minnesota ?
with thanks
Simon
PS I could not open BB8_MAS_RMA.tar.gz after downloading it
|
| no |
2008-02-09 17:07:34 |
Allan |
Showalter |
showalte@ohio.edu |
Ohio |
Question |
http://www.plexdb.org/modules/PD_general/tools.php? |
How do I look at the organ-specific expression profile of a rice gene in all the rice microarray experiments in your database? For example, any of the following rice genes: Os02g0763200, Os08g0334900 or Os06g0212500. |
| no |
2008-02-07 15:11:53 |
Matthew |
Moscou |
moscou@iastate.edu |
Iowa |
Bug report |
http://www.plexdb.org/404.php? |
The "Submit experiment with PLEX Express /BarleyExpress" takes me to a page that says "The page you requested can not be found." |
| no |
2008-01-21 16:28:57 |
Grant |
Cramer |
cramer@unr.edu |
University |
Question |
http://www.plexdb.org/modules/PD_general/tools.php? |
Hello,
I wanted to cluster the nearest transcripts (probesets) to one of my favorite probesets. The clustering tool was no longer there in the probe set expression details. What happened to it? Is this useful tool still available??? |
| no |
2007-12-21 03:57:42 |
Stefania |
Pilati |
stefania.pilati@iasma.it |
IASMA |
Bug report |
http://www.plexdb.org/404.php? |
hi,
I have noticed that a lot of links in your DB are not working (I can log-in only on certain pages; if I search an experiment, I cannot specify the species, but I have to specify the array type and so on).
I am submitting my experiment: I have saved and proceeded after the factor description and also the first hybridization description, and saved. I lost everything, except the first page.
Please, reply quickly as I am not going to continue with the submission in this way. |
| no |
2007-10-31 15:17:19 |
Greg |
Fuerst |
gsfuerst@iastate.edu |
USDA-ARS |
|
http://www.plexdb.org/404.php? |
The barley photo library is not available. |
| no |
2007-08-14 09:31:09 |
Rohan |
Lowe |
rohan.lowe@bbsrc.ac.uk |
Rothamsted Research |
Data error |
http://www.plexdb.org/modules/PD_general/downloadcgi.php?file=188 |
Re the datafiles associated with experiment FG2. I clicked on the link to download the expression data for the experiment. This downloaded sucessfully, however when I opened the FG2mas file which contains the signals and P values, I found that the p values are missing for chip 000241_MM-N-3, the final chip in the file.
Can you confirm this data is missing from the experiment and if so find a remdy for the situation. It would be useful to know the presence P values for this chip.
Thanks,
Rohan |
| no |
2007-07-27 07:06:39 |
Anette |
Henriksen |
anette@crc.dk |
Carlebserg Laboratory |
Question |
http://www.plexdb.org/modules/PD_general/download.php? |
How do I cite the use of plexdb in my manuscripts?
Best regards,
Anette |
| yes |
2007-06-18 04:01:16 |
hu |
wenhuo |
huwenhuo@gmail.com |
ncgr |
|
http://www.plexdb.org/modules/tools/get_seq.php? |
how can i get the annotation for rice 57K?
i just want the data of gene locus that coresponding to the points on the array.
can anyon tell me how to get it?
thanks in advance. |
| yes |
2007-06-08 05:46:39 |
Xiaoming |
Pang |
xmpang@163.com |
BJFU |
Database improvement |
http://www.plexdb.org/modules/PD_probeset/annotation.php?genechip=Poplar |
Under the directory of download for poplar, I found nothing. Is there really any poplar microarry data here? How can I access to the data? Thank you very much for the help. |
| yes |
2007-06-04 15:49:41 |
Haining |
Lin |
hlin@jcvi.org |
JCVI |
Barley1 22K download |
http://www.plexdb.org/modules/tools/get_seq.php? |
Dear PLEXdb Group,
Thank you for providing such useful microarray resources. Here, I have couple questions regarding barley1 22K data download.
1) I tried to get all the 21264 Barley1 gene chip sequences (both exemplar sequences and oligonucleotide probes) and their expression data from your website. It looked like I can get the exemplar sequences by copy/paste all the 21264 exemplars on the page http://www.plexdb.org/modules/tools/get_seq.php. Is this the right way or there is a better way that I\'ve missed?
2) I was not able to find a way to get the oligo probes all at once.
3) Neither was I able to get the expression data all at once.
Could you please help out?
Thank you very much for your attention.
Haining |
| yes |
2007-06-04 15:04:28 |
ling |
zhang |
lzhang1@wsu.edu |
washington state university |
Problem interpreting data |
http://www.plexdb.org/plex.php?database=Barley |
rice genome mapper website is not working at 6/4/07 |
| yes |
2007-05-22 21:03:01 |
Jinsong |
Pang |
pangjs542@nenu.edu.cn |
northeast normal university |
Problem searching BarleyBase |
http://www.plexdb.org/modules/documentation/downloadcenterhelp.php? |
Hello,
We are working on wheat expression profiling with Affymetrix wheat 61k genechip. After I got several thousands names of the different expressed genes, when I tried to get the information about the genes, I found I can only input the probe set designator one by one at http://www.plexdb.org/modules/PD_probeset/annotation.php?genechip=Wheat. Do you have a tool or a method, which I can batch download the information of genes, or the database of all genes?
thanks!
Jinsong pang
|
| yes |
2007-05-18 09:28:43 |
Grant |
Cramer |
cramer@unr.edu |
UNR |
None |
http://www.plexdb.org/modules/PD_dataSelection/experiments.php?class=experiment&expName=any |
VV7 is supposed to be publically available. Eventhough I am a co-author when I check experiments that are available to me, VV7 is not available or listed. There is another data set from Mark Thomas that was submitted 4 months ago and it is still not available to me. Please release this data to me. Thanks. |
| yes |
2007-05-18 09:08:55 |
Grant |
Cramer |
cramer@unr.edu |
UNR |
None |
http://www.plexdb.org/modules/PD_general/downloadcgi.php?file=182 |
You can release the data for VV1 now. The paper has been accepted for publication in Functional and Integrative Genomics! |
| yes |
2007-05-11 11:34:44 |
Roger |
Wise |
rpwise@iastate.edu |
ISU |
Dead link |
http://www.plexdb.org//modules/PD_general/feedbackcgi.php? |
page referer function in feedback doest go to problem page |
| yes |
2007-05-11 11:31:20 |
Roger |
Wise |
rpwise@iastate.edu |
ISU |
Dead link |
http://www.plexdb.org/modules/PD_probeset/probeplot.php?inputfile=Contig5108_s_at_BB10_probevalues.txt&experiment=BB10 |
No bar plots are shown for individual probes |
| yes |
2007-05-07 16:24:08 |
zhi |
zhang |
zhi.zhang@syngenta.com |
SBI |
|
http://www.plexdb.org/modules/PD_general/jobs.php? |
I can\'t open the page of Expression2Function. I sent an email to Lishuang Shen, but was returned.
Is there somebody I can ask?
Thanks
Zhi |
| yes |
2007-04-20 15:14:46 |
Roger |
Wise |
rpwise@iastate.edu |
ISU |
Data error |
http://www.plexdb.org/modules/PD_probeset/expressionplot.php?Accession_no=TA5&Probeset_name=Ta.10069.1.S1_at&Analysis=mas&chipdesign=Wheat |
no high res plot - waiting to be normalized? |
| yes |
2007-04-17 16:13:56 |
Clare |
Nelson |
jcn@ksu.edu |
KSU |
What I don't like about BarleyBase |
http://www.plexdb.org/modules/PD_dataSelection/FuncExpression/funcexpression.php? |
OK, all four of the links in the below-pasted text from the named referring page don\'t work for me, and I think I\'ll go find a site I can figure out how to use. It was an amusing forty-five minutes with y\'all, but I was hoping to analyze some data :-)
). Modules
A. Expression2GO -- Compare several types of gene lists for their distribution in GO classes among the lists.
B. Expression2Pathway -- Compare the ATH1 lists for their distribution in metabolic pathways.
C. Expression2GeneFamily -- Compare the ATH1 lists for their distribution among gene families.
D. Expression2Domain -- Compare the ATH1 lists for distribution among functional domains from InterPro.
(2). Input-- Data Sources and Formats
|
| yes |
2007-04-17 14:43:59 |
James |
Nelson |
jcn@ksu.edu |
Kansas State University |
Apparently broken functionality |
http://www.plexdb.org/modules/Your_Account/index.php? |
The page I was looking at, which doesn\'t have a feedback link, is
http://www.plexdb.org/modules/ontologies/go_window.php?
The GO hierarchy is not viewable as the instructions suggest. Clicking just shows and hides the top-level nodes, but doesn\'t open them up to show the children. The PO works OK, but not the GO -- at least in Firefox. |
| yes |
2007-02-26 00:57:52 |
Grant |
Cramer |
cramer@unr.edu |
UNR |
Data error |
http://www.plexdb.org/modules//PD_probeset/contig_grape.php? |
Plexdb suddenly did not provide the right annotation to the Vv grape probe set based on the blast. The blast results are wrong. Don\'t know what happened it was working earlier. |
| no |
2007-02-22 07:21:39 |
Gert-Jan |
de Boer |
g.de.boer@enzazaden.nl |
Enza Zaden R&D |
What I don't like about BarleyBase |
http://www.plexdb.org/modules//Your_Account/index.php?op=grpViewAll |
The view of the alignment of the probes and their target might be even more helpfull if the alignment could be saved as a genbank flat file. So the alignment could be studied in some more detail in any mol biol software package.
|
| no |
2007-02-12 13:40:52 |
Peter |
Hagedorn |
peter.hagedorn@risoe.dk |
Risø National Laboratory |
Data error |
http://www.plexdb.org/index.php? |
Dear PlexDB,
Concerning the BB9 dataset (Barley cv Morex inoculated with Fusarium graminearum and water as mock control). The normalized files (RMA or MAS) only mentions the .CEL file names. And when downloading the .CEL files for the experiment the zipped file only contains the .CEL files. The relation between the PlexDB IDs (BB9_H1, etc...) and .CEL files is missing. Therefore the relation between experimental factors and PlexIDs, as shown under experiment visualization. Is not as usefull. Now, I know that I can click each of the hybridization factors under experiment overview to get the relations, but it is not very \"high-throughput\". Also, for all the other barley experiments the RMA files simply contains this information in the first two rows. Could you update the BB9 experiement to follow this practice? |
