[BioC] total count filter cutoff (edgeR)

Daniel daniel.nicorici at gmail.com
Thu Jun 19 12:10:36 CEST 2014

Gordon K Smyth <smyth at ...> writes:

> Hi Mahnaz,
> Why don't you follow the advice of the edgeR User's Guide (as Mark has 
> suggested)?  All the case studies in the User's Guide describe how the 
> filtering was done in a principled way.
> Total count filtering is not so bad, but it is susceptible to being driven 
> by one library, especially by one library with a large sequence depth. 
> The procedure described by Mark and used in the guide is a compromise of 
> several considerations.
> BTW, there are newer versions of R and edgeR available than what you are 
> using.
> Best wishes
> Gordon


in case that one has miRNA (i.e. microRNA) data what is a good suggestion 
for the cpm cutoff? Is it the same like for RNA-seq?

I have not found a recommendation/case/example in the edgeR manuals/guides 
for miRNA-seq data analysis.

Best Wishes,

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