[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
>
Hello,
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,
Daniel
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