Hi,

I'm new in microarray data analysis and I have a quick and maybe "simple"
question about LIMMA and hope some one can help.

We have 6 Agilent data (3 controls and 3 treated samples). I like to use
LIMMA to figure out differentially expressing genes. I'm confused about
LIMMA statistics (logFC, AveExpr, t, P.Value, adj.P.Val, and B). Which one
researchers typically use to select differentially expressing genes? Can I
simple use adj.P.Val < 0.05 or P.Value < 0.05? Or, should I use combination
of these statistics? Thanks.

Amy

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