I am looking to test if a list of genes is significantly enriched in the differentially expressed dataset. I was wondering if there was a similar function to roast (Wu, et. al 2010) found in limma for digital gene expression data such as RNA-sequencing data. I am limited by the sample size and experimental design (4 samples from 2 tissues).

Jeff Hsu
Graduate Student
in Molecular Medicine at Case Western Reserve University

This can now be done in either the limma or edgeR packages.

In the limma package, camera() or roast() can be run on digital gene expression data after transforming with voom().

In the edgeR package, there are camera and roast methods than can be run directly on DGEList objects.