[BioC] total count filter cutoff

Ryan C. Thompson rct at thompsonclan.org
Wed Apr 30 23:49:27 CEST 2014

Yes, that is a good point that I forgot to mention. Thanks for 
correcting me.


On Wed 30 Apr 2014 02:25:09 PM PDT, Steve Lianoglou 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

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