Differential expression with continuous response variables

[Stefanocipo]

Hi,

Does anyone know any tools for differential expression using continuous response variables (or categorical but with more than two classes)? I only know SAMr and was wondering if there are better ones.

Thanks!

Stefano Cipollari

[dpryan]

DESeq2, edgeR, limma, etc. can all do that without any issue. In general, any tool that accepts uses a GLM should be able to handle that.

BTW, what ends up being better will depend on things like the number of samples you have.