[BioC] Interspecies differential expression of orthologs with Edger

[Tim Triche, Jr.]

I've been wondering a similar thing: suppose I use transcripts per million
(TPM) as a coherent estimate of abundance and feed it to limma/voom in
order to fit a multi-factorial blocked model in a poorly annotated organism
(draft genome and txome, but orthologs poorly characterized thus far).  It
appears to work properly in human and mouse samples (i.e. the top hits are
reasonable); is it sensible to generalize to non-model or poorly-annotated
organisms in this fashion?

Probably something that could be puzzled out given time, but since the
authors have likely addressed this before, a reference would be great.


Statistics is the grammar of science.
Karl Pearson <http://en.wikipedia.org/wiki/The_Grammar_of_Science>


On Mon, Aug 25, 2014 at 2:50 AM, assaf www <assafwww at gmail.com> wrote:

> 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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