Hi,
The plier and rmaexpress plug-ins calculates the probeset expression
values using information from the cel/cdf files. The plugins are
presented on the BASE plugin site
http://baseplugins.thep.lu.se/wiki/se.lu.thep.affymetrix How the
expression values are calculated is presented elsewhere (please follow
links from the plugin website).
The raw data for Affymetrix is stored in the original cel files and is
not stored in database tables like GenePix and other data. Affymetrix
related expression data is not stored in the database tables until the
creation of the first root bioassay set.
You do not need to create another affymetrix plugin if you are happy
with the algorithms provided by plier and rmaexpress. However, if you
need something else then you may need to write your own plugin (or help
us improve the current affymetrix plugin).
You may want to change the extended-properties.xml, some information on
this is available here,
http://base.thep.lu.se/chrome/site/doc/admin/extended-properties.html
The problem with using CDFs in your array design is most likely related
to missing reporters (probesets). Have you imported the reporters
associated with the design (CDF)?
Please read the information provided in the plugin site and
http://base.thep.lu.se/chrome/site/doc/user/getting_started.html (nice
example on the workflow in BASE with references to Affymetrix data).
And, of course, you can also use the mailing list.
Cheers,
Jari
Reha Yildirimman wrote:
Hello,
like some other people I am trying to import data from affymetrix CEL
files.
Searching the archive I have read that people use the RMAExpress and PLIER
plugins. As far as I understood the plug-in extracts/calculates the
intensities but
where are those data stored, since the associated raw data type for
affymetrix has
no database table definition?
Furthermore, are those intensities the stated MEAN values inside the CEL
file
and are extracted intensities for each coordinate/probe or only for
probe sets ?
I have another approach and if that seems ineffective to you please drop
me a line!
My approach is to change the affymetrix data type inside the
raw-data-type.xml
from a simple file-definition to a database-definition like the other
data-types defined
inside the xml.
I added properties for the values: MEAN (float), STDV (float), NPIXELS
(float)
To be able to import data via a base-plugin from a CEL file each data
line has to have
an association to a reporter - thus I added a column holding the
ProbeSet ID for each
CEL file.
My problem is that when I associate a CDF file to an array design -
which I need for
reference purpose - it states under Properties:
Features: Yes(0)
This makes the raw data importer fail with:
Item not found: Feature[row=null, column=null, block=null,
metaGridX=null, metaGridY=null] on line 2
If I take out the connection to the CDF - thus turning the Feature
property to No - the raw data importer works.
How can I get around the problem without having to add to each line
inside the CEL file fake numbers for the features
row, column, block, ...
Thanks alot in advance.
Best,
Reha
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Jari Hakkinen, PhD
Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics phone: +46 (0)46 2229347
Lund University fax: +46 (0)46 2229686
Solvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se
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