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
> >
> > _______________________________________________
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> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>

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