[BioC] Interspecies differential expression of orthologs with Edger

Gordon K Smyth smyth at wehi.EDU.AU
Tue Aug 26 01:28:09 CEST 2014

Dear Assaf,

In principle, one would incorporate gene length into the edgeR offset 
matrix, and this would eliminate any length-bias.

Best wishes

> Date: Mon, 25 Aug 2014 12:50:36 +0300
> From: assaf www <assafwww at gmail.com>
> To: bioconductor at r-project.org
> Subject: [BioC] Interspecies differential expression of orthologs with
> 	Edger
> Dear Edger developers and users,
> I would like to compare transcription levels of orthologous genes belonging
> to different species, in order to find significant species-dependent
> changes in  transcription levels. I though of using Edger for such analysis.
> Specifically, I have the read-counts data for several RNA-Seq samples, for
> 2 different species (e.g., read counts produced by Htseq-count, and Rsem).
> I would like to ask:
> 1) because Edger uses CPM values, which are not normalized by gene-length,
> and because the length of orthologous genes differ, it would lead to a
> serious length-dependet bias, and I would ask how to normalize for that.
> 2) if the above length-bias can be eliminated, and the compared genes are
> true orthologs, are you aware of any other major problems that should be
> considered in the above case ?
> Thanks in advance,
> Assaf

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