[BioC] Vsn transformation repeatability

Paolo Innocenti 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!


Paolo Innocenti
Department of Animal Ecology, EBC
Uppsala University
Norbyvägen 18D
75236 Uppsala, Sweden

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