[BioC] filtering or not filtering?

James MacDonald jmacdon at med.umich.edu
Mon Dec 8 23:48:22 CET 2008

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.



James W. MacDonald, M.S.
Hildebrandt Lab
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
>>> "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.


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