[BioC] Very low P-values in limma

Vincent Carey stvjc at channing.harvard.edu
Wed Oct 21 20:00:48 CEST 2009

This is not a very precise description of the activity.  Are you sure
you are looking at the right coefficient for your test?  If you do
topTable(fit) without specifying the coef you may be looking at
p-values for the wrong test.  Read the topTable documentation
carefully and be sure you have set up the design matrix correctly.

On Wed, Oct 21, 2009 at 1:36 PM, Paul Geeleher <paulgeeleher at gmail.com> wrote:
> 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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