[BioC] comparing affymetrix and agilent microarray data

Jarek Bryk bryk at evolbio.mpg.de
Tue May 26 13:45:07 CEST 2009

Hello again,

I have two datasets acquired by running the same samples from two 
populations on both affymetrix and agilent (single-color) microarrays. I 
want to find genes that are consistently differentially expressed 
between the two populations in both platforms.

For analysis of the affymetrix data, I used the custom CDF file from the 
Dai lab 
, which greatly facilitates interpretation of the data (as it collapses 
the probe and transcripts from the same gene onto single Ensembl gene 
ID). Now I would like to compare this result to my agilent data (to sort 
of validate affy results by the agilent).

Is there any mapping file similar to the CDF for affy that I could use 
for my agilent data? I've looked, and I don't think there is... If not, 
what would be best way to compare the two datasets? Filter the agilent 
probes for the differentially expressed genes from the affy data and 
then compare the populations?

Ideas would be very welcome :-)


   Jarek Bryk
   Max Planck Institute for Evolutionary Biology
   August Thienemann Str. 2 | 24306 Plön, Germany
   tel. +49 4522 763 287 | bryk at evolbio.mpg.de

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