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Old 04-09-2013, 06:39 AM   #1
Junior Member
Location: Connecticut

Join Date: Apr 2013
Posts: 4
Default RNA Seq: differential gene expression with multiple factors


I'm looking to assess differential gene expression using Illumina HiSeq reads. I have a two-factor experimental design (three divergent fish populations each treated at two salinities). I would like to assess differential expression using a two-way model - specifically I want to pinpoint genes for which there are significant interaction effects.

Does anyone know if any of the (many) RNA seq tools available can run a model of this kind (probably a generalized linear model) using these data?

Thanks so much.
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