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@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@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
>
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-- 
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//   our desire; the more we see, the more we are capable
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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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