Hi folks, I'm analyzing microRNA data using limma and I'm wondering about
the validity of the p-values I'm getting out. Its a simple 'Group A Vs Group
B' experimental design. 4 arrays in one group, 3 in the other and 4
duplicate spots for each miRNA on each array.

The lowest adjusted p-values in the differential expression analysis are in
the region of 10^-7.

Its been pointed out to me that plugging the point values from each sample
into a regular t-test you get p=0.008, which then also needs to take the
multiple test hit. Can anybody explain why limma is giving me such lower
values and if they are valid?

I can provide more information if required.

Thanks,

Paul.

-- 
Paul Geeleher
School of Mathematics, Statistics and Applied Mathematics
National University of Ireland
Galway
Ireland

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