[BioC] voom

[Ina Hoeschele]

thanks, Wolfgang, I realize that. I did not have time yesterday but will do some more investigating myself today and if nothing shows up I will provide code etc.. 
Ina

----- Original Message -----
From: "Wolfgang Huber" <whuber at embl.de>
To: "Ina Hoeschele" <inah at vbi.vt.edu>
Cc: "bioconductor" <bioconductor at stat.math.ethz.ch>, "Bioconductor mailing list" <bioconductor at r-project.org>
Sent: Friday, July 12, 2013 9:39:23 AM
Subject: Re: [BioC] voom

Dear Ina

thanks. The problem report is a little unspecific… I presume that the people who could respond to this would need to know
- the exact code you are running
- version numbers (sessionInfo)
- the plots that you are getting
- (ideally and I am not sure it's needed although it doesn't harm) the offending data, in anonymised form.

Best wishes
	Wolfgang


On 11 Jul 2013, at 22:21, Ina Hoeschele <inah at vbi.vt.edu> wrote:

> Hi,
>  I'm using limma's voom function on a (human) RNAseq dataset (regular transcript based count matrix). When I do an MDS plot on the input count matrix, all looks "normal". When I do the same plot on the output log CPM matrix (E), the samples (N=329) cluster strongly into two groups of about equal size. This happens no matter how I run voom (with or without design matrix, passing count matrix and adjusted lib sizes, or DGE obj).
> Thanks, Ina
> 
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