This thread has accumulated a good number of opinions and speculations what the best filter criterion and cutoff value is. The ?genefilter? vignette (I mentioned it previously) "Diagnostics for independent filtering? [1] provides rational criteria for deciding in a data-dependent manner. Kind regards Wolfgang [1] http://bioconductor.org/packages/release/bioc/html/genefilter.html On 30 Apr 2014, at 23:25, Steve Lianoglou <lianoglou.steve at="" gene.com=""> wrote: > Hi, > > On Wed, Apr 30, 2014 at 1:11 PM, Ryan C. Thompson <rct at="" thompsonclan.org=""> wrote: >> Filtering on raw counts has a statistical motivation, i.e. something like >> "we can't do statistics with less than X reads". Filtering on CPM is >> sometimes just used as a proxy for count-based filtering, but sometimes it >> also has a biological motivation, i.e. "we believe that CPM < X represents >> biological noise transcription rather than genuine regulated transcription >> relevant to the biological system in question". So you have to consider what >> your goals are for filtering and choose an appropriate method. > > Even still, in the "biological motivation" case: if you want to use > CPM, shouldn't you really prefer {R|F}PKM so you don't "enrich" for > removal of lowly expressed short transcripts while letting lowly > expressed long transcripts slip through? > > -steve > > -- > Steve Lianoglou > Computational Biologist > Genentech > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Thanks so much all of you for good recommendation, really apppriciate you time. Regards, Mahnaz On Mon, May 5, 2014 at 4:33 PM, Wolfgang Huber <whuber@embl.de> wrote: > This thread has accumulated a good number of opinions and speculations > what the best filter criterion and cutoff value is. > The "genefilter" vignette (I mentioned it previously) "Diagnostics for > independent filtering" [1] provides rational criteria for deciding in a > data-dependent manner. > > Kind regards > Wolfgang > > [1] http://bioconductor.org/packages/release/bioc/html/genefilter.html > > On 30 Apr 2014, at 23:25, Steve Lianoglou <lianoglou.steve@gene.com> > wrote: > > > Hi, > > > > On Wed, Apr 30, 2014 at 1:11 PM, Ryan C. Thompson <rct@thompsonclan.org> > wrote: > >> Filtering on raw counts has a statistical motivation, i.e. something > like > >> "we can't do statistics with less than X reads". Filtering on CPM is > >> sometimes just used as a proxy for count-based filtering, but sometimes > it > >> also has a biological motivation, i.e. "we believe that CPM < X > represents > >> biological noise transcription rather than genuine regulated > transcription > >> relevant to the biological system in question". So you have to consider > what > >> your goals are for filtering and choose an appropriate method. > > > > Even still, in the "biological motivation" case: if you want to use > > CPM, shouldn't you really prefer {R|F}PKM so you don't "enrich" for > > removal of lowly expressed short transcripts while letting lowly > > expressed long transcripts slip through? > > > > -steve > > > > -- > > Steve Lianoglou > > Computational Biologist > > Genentech > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]