[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
(http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_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 Plön, Germany
tel. +49 4522 763 287 | bryk at evolbio.mpg.de
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