Question: cpm cutoff (edgeR) [was: total count filter cutoff (edgeR)]
gravatar for Gordon Smyth
5.5 years ago by
Gordon Smyth39k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth39k wrote:
Dear Daniel, The guidelines are the same for miRNA-seq as for RNA-seq. At its simplest, you simply need a reasonable minimum number of counts in at least some samples. At a minimum, I think you would want at least 5 counts, maybe more, in each sample in which the gene in expressed. So, if your sequencing depth is about 20 million reads per sample, you might ask for cpm>0.3 (equivalent to 6 reads). If your sequence depth is 10 million read per sample, you might ask for cpm>0.6 (again equivalent to 6 reads). It's not rocket-science. It's all quite rough as the exact cutoff isn't important. Best wishes Gordon > Date: Thu, 19 Jun 2014 10:10:36 +0000 > From: Daniel <daniel.nicorici at=""""> > To: <bioconductor at=""""> > Subject: Re: [BioC] total count filter cutoff (edgeR) > > > 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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
sequencing mirna edger • 2.4k views
ADD COMMENTlink written 5.5 years ago by Gordon Smyth39k
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