[BioC] Save top genes used in plotMDS (edgeR)

Gordon K Smyth smyth at wehi.EDU.AU
Tue Jan 28 23:40:50 CET 2014

Dear Maria,

No you can't do this.  The reason why we don't tell you which were the top 
genes is that the selection of top genes is different for every pairwise 
comparison between the samples.  For example, if you are plotting ten 
samples, then there are choose(10,2) = 45 different lists of top genes.

Best wishes

> Date: Tue, 28 Jan 2014 09:50:50 +0100
> From: Maria Jesus Garcia <mj.garcia.pereira at gmail.com>
> To: bioconductor at r-project.org
> Subject: [BioC] Save top genes used in plotMDS (edgeR)
> I would like to save the top genes that best distinguish the samples used
> to construct the MDS in edgeR but I don't know how. Is there a way to do it?
> Thanks in advance
> -- 
> María Jesús García Pereira

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