[BioC] Analysis for only 2 replicates

[Khan, Sohail]

Dear list,

I have 2 -wt and 2-mutant samples done on Affymetrix chips.
Could you suggest the best way to analyze this experiment? Is averaging both replicates and picking genes based on fold change good??
Thanks for any suggestions.


Sohail Khan
Scientific Programmer
COLD SPRING HARBOR LABORATORY
Genome Research Center
500 Sunnyside Boulevard
Woodbury, NY 11797
(516)422-4076