[BioC] Very low P-values in limma
Thomas.H.Hampton at Dartmouth.edu
Wed Oct 21 22:04:57 CEST 2009
I too find it very odd that a multiple hypothesis correction
apparently reduces P values. One possibility is that
the duplicate spot weighting in limma is somehow doing a really
superior job compared to a simple t test
that might view duplicates on different arrays as the same thing as
duplicates on the same array.
On Oct 21, 2009, at 1:36 PM, Paul Geeleher wrote:
> Hi folks, I'm analyzing microRNA data using limma and I'm wondering
> 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
> into a regular t-test you get p=0.008, which then also needs to take
> multiple test hit. Can anybody explain why limma is giving me such
> values and if they are valid?
> I can provide more information if required.
> Paul Geeleher
> School of Mathematics, Statistics and Applied Mathematics
> National University of Ireland
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