[BioC] filtering or not filtering?

Jenny Drnevich drnevich at illinois.edu
Tue Dec 9 17:03:40 CET 2008


Hi Yisong,

You want to filter AFTER doing the eBayes() correction, but BEFORE 
doing the multiple test correction. This way, eBayes() correctly 
estimates the "average" variability of the genes, but you only have 
to do the multiple test correction on the genes for which you can 
rationally create a filter.

Cheers,
Jenny

At 05:26 PM 12/8/2008, Yisong Zhen wrote:
>It seems that I have to read carefully the Limma module. I though it will
>reduce the false positive ( and following step about multiple- testing
>correction) when filtered out those genes with low expression constantly and
>genes with low CV.
>Yisong
>On Mon, Dec 8, 2008 at 3:48 PM, James MacDonald <jmacdon at med.umich.edu>wrote:
>
> > Hi Yisong,
> >
> > One of the assumptions behind the eBayes() step used by limma is that you
> > have not filtered out any genes (e.g., the eBayes()  step estimates the
> > 'average' variability of the genes on your microarray, and if you filter
> > some out, you can affect this estimate).
> >
> > As for how to filter, this has been the subject of many many conversations
> > on this list, and I think there are as many opinions as subscribers ;-D.
> > IMO, whatever you do you should have a reasonable rationale for what you
> > have done, which is true for most steps in a given analysis. Since I can't
> > give you a rationale I won't belabor you with my opinion either.
> >
> > Best,
> >
> > Jim
> >
> >
> >
> > James W. MacDonald, M.S.
> > Biostatistician
> > Hildebrandt Lab
> > 8220D MSRB III
> > 1150 W. Medical Center Drive
> > Ann Arbor MI 48109-0646
> > 734-936-8662
> > >>> "Yisong Zhen" <zhenyisong at gmail.com> 12/08/08 5:25 PM >>>
> >  Dear Bioconductor users,
> >
> > Before I performed Limma analysis, should I do non specific filter or not?
> > If we should do filter before Limma step, how do I determine the cut-off
> > for
> > filtering-function? For example, If I use Co-efficient of  Variability (CV)
> > as filtering criteria, how should I set the cut-off? arbitrarily?
> >
> > Thanks in advance.
> >
> > Yisong
> >
> >        [[alternative HTML version deleted]]
> >
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>
>
>
>--
>//-----------------------------------------------------------------------------------------
>//   We have a hunger of the mind which asks for knowledge
>//   of all around us, and the more we gain, the more is
>//   our desire; the more we see, the more we are capable
>//   of seeing.
>//----------------------------------------------------------------------------------------
>
>Yisong Zhen, Ph.D (Davidson Lab)
>Molecular & Cellular Biology
>Molecular Cardiovascular Research Program
>University of Arizona
>1656 E. Mabel, MRB 317
>Tucson, AZ 85724 USA
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
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e-mail: drnevich at illinois.edu



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