Question: total count filter cutoff (edgeR)
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gravatar for Daniel
5.2 years ago by
Daniel10
Finland
Daniel10 wrote:
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
mirna edger • 580 views
ADD COMMENTlink written 5.2 years ago by Daniel10
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