Is there an R statistical program for calculating differential gene expression with paired RNA-seq data?

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Nailê Damé-Teixeira

Dear Dr Delker,

Did you try the DESeq2?

Naile

Steffen Priebe

This should be possible using generalized linear models. There are used in the new version of DESeq (DESeq2) and edgeR.

See section 5.4 in the DESeq manual:

http://www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.pdf

Don A Delker

Thank you Naile and Steffen. I will give it a try.

Aliaksei Z Holik

To supplement Steffen's answer, here's the link to edgeR manual. Chapter 3.4 describes the paired design.

http://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf