[BioC] limma

[Anita Grigoriadis]

Hi, I am using limma to identify differentially expressed genes on 4
different platforms (CodeLink, Affymetrix, Agilent and an inhouse cDNA
array), 2 RNA samples, 3 replicates for each on the one color
microarrays, 6 replicates for the two color arrays.   I used limma with
fdr to adjust the p-value, and my result of differential genes from
Affymetrix to the inhouse cDNA array was from 8000 to 500 differentially
expressed probe sets. My  question: is it reasonable to apply the same
Thanks for some advice
Anita


Dr Anita Grigoriadis
The Breakthrough Toby Robins
Breast Cancer Research Centre,
Institute of Cancer Research,
237 Fulham Road,
London, SW3 6JB