[BioC] Very low P-values in limma

Gordon K Smyth smyth at wehi.EDU.AU
Fri Oct 23 04:51:24 CEST 2009

> [BioC] Very low P-values in limma
> Thomas Hampton 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.

It would be odd if it did, but it doesn't.

> 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.

It doesn't.  See the documentation.

Best wishes

> Tom

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