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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