[BioC] Filtering before differential expression analysis of microarrays - New paper out

James W. MacDonald jmacdon at med.umich.edu
Mon Jan 12 15:25:02 CET 2009

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 

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.



> Many thanks
> Dan

James W. MacDonald, M.S.
Hildebrandt Lab
1150 W. Medical Center Drive
Ann Arbor MI 48109-5646

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