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
begin:vcard
fn:Reha Yildirimman
n:Yildirimman;Reha
org:Max Planck Institute for molecular genetics;Lehrach AG Herwig
adr:;;Ihnestr. 63-73;Berlin;;14195;Germany
email;internet:[EMAIL PROTECTED]
tel;work:+49-30-84131682
url:http://www.molgen.mpg.de
version:2.1
end:vcard
-------------------------------------------------------------------------
This SF.net email is sponsored by: Splunk Inc.
Still grepping through log files to find problems? Stop.
Now Search log events and configuration files using AJAX and a browser.
Download your FREE copy of Splunk now >> http://get.splunk.com/
_______________________________________________
The BASE general discussion mailing list
basedb-users@lists.sourceforge.net
unsubscribe: send a mail with subject "unsubscribe" to
[EMAIL PROTECTED]
