[BioC] Filtering before differential expression analysis of microarrays - New paper out (James W. MacDonald)
drnevich at illinois.edu
Tue Jan 13 18:31:41 CET 2009
In general, you can filter by subsetting a MArrayLM object the exact
same way as you would an ExpressionSet object. If you have any
trouble, please post the code that you are trying to use.
At 10:47 AM 1/13/2009, Sherosha Raj wrote:
>I"m sorry if this is a simple question, but how does one go about
>filtering after the eBayes step since the resulting object is of the
>I am used to filtering expression sets directly.
>Thank you very much!
> > ---------- Forwarded message ----------
> > From: "James W. MacDonald" <jmacdon at med.umich.edu>
> > To: Daniel Brewer <daniel.brewer at icr.ac.uk>
> > Date: Mon, 12 Jan 2009 09:25:02 -0500
> > Subject: Re: [BioC] Filtering before differential expression
> analysis of microarrays - New paper out
> > Hi Dan,
> > Daniel Brewer wrote:
> >> Hi,
> >> There is a new paper out at BMC bioinformatics that seems to justify the
> >> use of filtering before differential expression analysis is performed
> >> (Hackstadt & Hess BMC Bioinformatics 2009, 10:11 -
> >> http://www.biomedcentral.com/1471-2105/10/11/abstract). Specifically
> >> filtering by variance and detection call. I have got the impression
> >> from this list that the general opinion is that one should only filter
> >> out the control genes before testing. I was wondering if anyone had any
> >> opinions on this paper and the topic in general.
> > I'm sure people do have opinions about this topic ;-D
> > The reason people have so many opinions is because it isn't a
> simple question, and it depends on what you consider important.
> > If you are just trying to limit the number of multiple
> comparisons to increase power, then filtering first is probably the way to go.
> > If you are concerned with the accuracy of the FDR estimates, then
> filtering first may not be ideal.
> > If you are using limma (Hackstadt and Hess used multtest), then
> you should filter after the eBayes step but before the FDR step, as
> an assumption of the eBayes step is that all of the data from the
> chip are available.
> > Unless of course you are concerned about the accuracy of the FDR
> estimates, in which case... well you see the point.
> > With microarray data analysis the arguments for and against a
> particular way of doing things can shed more heat than light, as
> nobody really knows the underlying truth, and the measures we use
> are really far removed from the actual phenomenon we are testing.
> > Best,
> > Jim
> >> Many thanks
> >> Dan
> > --
> > James W. MacDonald, M.S.
> > Biostatistician
> > Hildebrandt Lab
> > 8220D MSRB III
> > 1150 W. Medical Center Drive
> > Ann Arbor MI 48109-5646
> > 734-936-8662
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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
1201 W. Gregory Dr.
Urbana, IL 61801
e-mail: drnevich at illinois.edu
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