[BioC] [limma] [Rfit] [samr] Gene expression distribution using lmFit and eBayes

Jérôme Lane jerome.lane at criucpq.ulaval.ca
Thu Nov 21 23:42:21 CET 2013


   The 3/4 of my microarray gene expressions have non normal distribution with
   most of p-values after Shapiro test under 10x-5.

   I tried linear ranked regression from rfit (no normality assumption for
   residues)  from Rfit package for adjustment of covariables +  SAM (non
   parametric) from samr package but results where not as biologically relevant
   as lmFit + eBayes could provide.

   I know that lmFit function can analyses gene expression not strictly normal,
   but what is the limit ?

   Is it statistically relevant to use lmFit + eBayes according to my data ?

   Best regards,

   Jérôme Lane

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