Question: cpm cutoff (edgeR) [was: total count filter cutoff (edgeR)]
0
gravatar for Gordon Smyth
5.2 years ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k 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="" gmail.com=""> > To: <bioconductor at="" stat.math.ethz.ch=""> > 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 • 2.3k views
ADD COMMENTlink written 5.2 years ago by Gordon Smyth38k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 248 users visited in the last hour