Hello:

I have created and annotated a DGEList from RNA-seq data.

I would like to try EGSEA, however the DGEList$genes$entrezgene column has ~900 'NA' values.

Is there a way to remove rows with entrezgene values of 'NA' from the DGEList?

Thank you

You can subset a DGEList as if it was a matrix. For example:

i <- is.na(dge$genes$entrezgene)
dge <- dge[!i, ]

This removes all the rows for which the Entrez Gene ID is NA.