1. Registration with PLEXdb as an official user.
2. Your experimental design.
3. Your protocols.
4. The raw data from Affymetrix MAS 5.0 Suite. *.CEL
and *.EXP files are required for each hybridization.
2.4. Which operating systems can be used for making
submissions?
Windows, MAC and Linux all work, provided you have a
compatible browser installed. PLEXdb has been tested
successfully with all popular browsers.
2.5. Which browser works best for the submission process?
Any popular browser should work fine for the submission
process. You will be safest if you use Firefox,
Safari, Mozilla, or Internet Explorer.
2.6. Why does PLEX Express require experiment factor and
factor levels?
PLEX Express needs the experiment factors and their levels
explicitly specified. This is essential for other users to
understand the experiment, as well as helping PLEXdb to
analyze and present the data in a more meaningful and
easy-to-understand way. As more experiments are added to
PLEXdb, this will also help users to compare results across
experiments.
2.7. Must I finish a submission in one sitting? Can I stop
at some point and resume submission later?
Yes, you may stop at any time point and resume submission
later.
2.8. Can I add more experiment factors or factor levels to
my finished submission?
No, this is one of the few fields that cannot be changed
without resubmission. You can rename fields and values
however (see section 2.9)
2.9. Can I change the names of the experiment
factors/level?
Changing the names of factors or factor levels is allowed
before finalizing your experiment submission, provided
that this change will not change the numbers of factors
and levels.
2.10. Any recommendations for a smooth submission?
Submission requires careful checking before presenting
your results to other researchers in PLEXdb. Some things to
keep in mind are:
- Specify the number of factors and the levels of each
factor carefully. Once submitted, this information can't
be changed without re-doing the entire submission.
The only allowable modifications are typo-corrections or
renaming the factors and levels.
- CAREFULLY check your file name association and sample
association with the treatment before finalizing your
submission. Complete all fields in the
"Plant Sample Description" page that you have
information for.
- Any revisions, except for text changes, after
"Finalize" will incur much effort at both sides
from submitter and administrator, and greatly delay the
processing of your data in the best situation. Significant
revisions may require re-submission.
2.11. I have many samples and they are very similar; how
can I submit them quickly?
Specifiying pllant sample information is the most
time-consuming part for experiment submission. To help
ease this process, the submitter an copy existing plant
sample records for editing. This means the submitter will
need to just fill in one plant sample record completely,
and for all subsequent samples, use this first record as
a "template", changing the name and any other
field that differ from one sample to the next.
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3. MANAGEMENT OF ACCOUNT, EXPERIMENTS AND DATA ACCESSIBILITY
3.1. Why register with PLEXdb? How to register with PLEXdb?
Only registered users can submit their experimental data,
access non-public data, and perform batch downloads of data.
3.2. What is the purpose of group management?
Group management lets users grant data access to their
collaborators before the data is released to the public.
For example, a user could create a group consisting of
consortium members worldwide then give that group permission
to view experiment data submitted by that user.
3.3. Will my experiment data be visible to the public
immediately? Can I control who will be able to access my
submission before my results are published?
PLEXdb encourages data sharing with the whole community.
But we understand your need for keeping data private until
your results are published. To make your data visible ONLY
to users that you select, please designate your submission
as "Private" or "Group Consortium"
when you submit your experiment using PLEX Express. Then you
can use group management to grant access to people you
select.
3.4. How can I grant access to my private data to other
users? Can I delete users from the access list?
Under the "Your Account" menu, select
"Group Management", then you can create, edit,
or remove groups. You can also add or delete users from your
own groups.
To grant access to an experiment to a given group, under
the "Your Account" menu, select
"Experiment Management", follow the link
Associate groups with the experiments.
3.5. What if I designated my data as private when making
my submission, but later on I need to let selected people
to access it?
You can create groups, and associate experiments with the
groups as explained in 3.4.
3.6. Can I get all data for an experiment with batch
download? What types of data will be downloadable?
Yes, we make all data available in compressed format for
batch downloading. There are several common types of data:
EXP, CEL (Probe-pair level information),
DAT(images read by Affymetrix scanner), the normalized
expression value files (using MAS 5.0 and RMA methods),
and a table linking hybridization data files to each
treatment and replication.
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4. MICROARRAY EXPERIMENT AND PROBE SET QUERIES
4.1. How can I find an experiment? Can I view all experiments
stored in PLEXdb?
You can query for experiments on the
"Experiment
Query" page. You will be able to see your own
experiments, experiments you have been given permission to
see by colleagues, and all of the public experiments.
4.2. I have sequence from other species, how can I find its
homologous exemplar sequences and their expression in the
supported GeneChips?
The best place to go is the
"PLEXdb
Blast" page. Input your sequence and click 'BLAST'.
From the results page pick your sequence-of-interest for a
detailed view.
4.3. My search returned a list of probe sets, can I get the
probe-level data for them?
[Needs research]
4.4. I would like to analyze a data set obtained from my
queries locally, what format is the data in?
You may now download them as tab-delimited text files,
either as expression, or as annotation. This plain-text
format can be easily imported to most microarray tools.
4.5. Where can I get all information for a given exemplar
sequence or probe set?
Detailed information for probe sets or exemplars is available
on the annotation page. For example, here is the annotation
page for the Barley1 probes set,
Contig1637_at.
This page lists everything available within PLEXdb along
with links to other databases on online resources for that
probeset and microarray.
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