Dear All:

I'm trying to identify genes that are differentially expressed in 4
different treatments vs Control. First, I applied
*pairwise.comparison*(simpleaffy library) to my data, and then, just
to compare both results, I
tried *lmFit* and *eBayes* (from limma library). I was wondering which
method is best, because although  pairwise.comparison applies a t-test, it
doesn't include Bonferroni correction. On the other hand I'm not sure
whether fitting the data to a linear model using lmFit and eBayes is more
convenient. I have also found another library(maanova) that uses Anova and
it's also suitable for DNA microarray analyzes.

I will appreciate any hint about which method to choose.

Thanks a lot,

Avhena

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