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 (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/ge nomic_curated_CDF.asp) , 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 :-) cheers jarek -- Jarek Bryk Max Planck Institute for Evolutionary Biology August Thienemann Str. 2 | 24306 Pl?n, Germany tel. +49 4522 763 287 | bryk at evolbio.mpg.de