removing genes with low level expression

[tinguzman]

Hi,

I'm currently using the trinity package for RNAseq analysis. A little help here. If I wanted to run EdgeR with all the genes in my trinity assembly, is there a way to filter the DE results to remove genes with very low level expression. I know that I can use the output from filter_by_rsem, then just manually edit the DE results using excel, but I'm wondering if there is a script that will work directly on the DE results.

hope you could help.


thanks,
Christine

[Gordon Smyth]

See any of the case studies in the edgeR User's Guide. You need to do the filtering at the beginning of the DE analysis rather than at the end.