[BioC] Analysis for only 2 replicates

[James W. MacDonald]

Khan, Sohail wrote:
> 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.

I would recommend using limma to analyze these data. Even though you 
only have two replicates, accounting for variability is better than 
ignoring it altogether.

Best,

Jim


> 
> 
> Sohail Khan Scientific Programmer COLD SPRING HARBOR LABORATORY 
> Genome Research Center 500 Sunnyside Boulevard Woodbury, NY 11797 
> (516)422-4076
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623