Question: total count filter cutoff (edgeR)
gravatar for Daniel
5.2 years ago by
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
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 270 users visited in the last hour