[BioC] Vsn transformation repeatability
paolo.innocenti at ebc.uu.se
Fri Oct 31 10:50:37 CET 2008
Wolfgang Huber wrote:
> 1. You say "number of ... differentially expressed genes for a
> particular FDR changes with each run". By how much? The variation should
> be tiny (negligible?), otherwise I would be worried about the stability
> of your method to compute differential expressedness, and FDR.
I use the simplest possible approach in limma (one factor with 2 levels)
following the userguide. The problem seems to be that the distribution
of adjusted p.values is rather odd: instead of having a peak at 0, I
have a clear peak between 0.05 and 0.1, so that a minimum difference in
the normalization have a rather big effect on the number of my
differentially expressed genes (I fixed the cutoff at 0.1).
The difference is the order of 5% of d.e. probesets found (range between
1700 and 1900 on a total of 18000).
> Please see the code example below for how to deactivate the subsampling.
Deactivating subsampling fix the problem!
Thank you very much!
Department of Animal Ecology, EBC
75236 Uppsala, Sweden
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