[BioC] edgeR - estimateGLMCommonDisp - warnings - huge logFC

[Robert Castelo]

hi,

this very recent correspondence published at Nature Biotech may help
you, and possibly help others interested in this thread, to frame some
of the more general remarks made by Gordon Smyth in his last message:

Hansen KD, Wu Z, Irizarry RA & Leek JT
Sequencing technology does not eliminate biological variability
Nature Biotechnology 29, 572–573 (2011) doi:10.1038/nbt.1910
Published online 11 July 2011
http://www.nature.com/nbt/journal/v29/n7/full/nbt.1910.html

cheers,
robert.

On Fri, 2011-07-08 at 08:18 +0000, Filippis, Ioannis wrote:
> Hi,
> 
> I am using edgeR for a 2x2 factorial design (Strain*Treatment) without any replicates and the estimateGLMCommonDisp and glmFit functions.
> 
> When I run estimateGLMCommonDisp, I get warnings
> 1: In optimize(f = fun, interval = interval^0.25, y = y,  ... :
>   NA/Inf replaced by maximum positive value
> and when I run glmFit and then glmLRT, I get huge fold change values for some genes.
> 
> However, if I do a pairwise exactTest for the samples examined for the above contrast, the fold change for that genes is high but normal.
> 
> I would really appreciate any feedback on the cause of warnings and huge logFC.
> 
> Many thanks for your help.
> 
> Best,
> Ioannis
> 
> 	[[alternative HTML version deleted]]
> 
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