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Old 08-14-2014, 03:19 AM   #1
tinguzman
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Location: Philippines

Join Date: Aug 2014
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Default removing genes with low level expression

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
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Old 08-18-2014, 01:27 AM   #2
Gordon Smyth
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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.
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