[BioC] Question on filtering in the Category package

[Boel Brynedal]

Dear list,

I have a theoretical question regarding Filtering on Variation in the
Category package. I've performed an analysis that closely resembles the
Vignette, but I am still a bit uncertain about the filtering. 
In the Vignette the following code is used:
lowQ<-rowQ(eset,floor(0.25*NumArrays)) 
upQ<-rowQ(eset,ceiling(0.75*NumArrays))
iqrs<-upQ-lowQ
select<-(upQ-lowQ)>0.5

My question is, why is this filtering necessary? I have performed my
analysis without filtering, and the results where strange. 
My guess is that this filtering is intended to eliminate the probe-sets
that aren't expressed at all (and would cause category's containing them
to be associated). But the reason for eliminating the probe-sets with
the highest variability is less clear for me. Would these include probe-
sets where something has gone wrong, or probe-sets that are not
expressed at all in some, but not all, arrays? 
What have I missed?

What kind of filtering are you using, and why?

Is there an article out there discussing the variability, and cause of
the variability, on arrays? 

Any comments would be helpful.
Thank you!

Best,
Boel Brynedal


--~*~**~***~*~***~**~*~--
Boel Brynedal, MSc, PhD student
Karolinska  Institutet
Department of Clinical neuroscience

Karolinska University hospital Huddinge
Division of Neurology, R54
141 86 Stockholm
SWEDEN
Phone: +46 8 585 819 27
Fax:   +46 8 585 870 80
E-mail: boel.brynedal at ki.se