| Resolved |
Date |
First Name |
Last Name |
Email |
Institution |
Subject |
Webpage |
Comments |
| 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? |
