[BioC] Question on filtering in the Category package

[Wolfgang Huber]

Dear Boel,

as you say, the filtering is intended to eliminate the probe-sets
whose targets are not expressed and hence that are uninformative / only 
contribute noise.

 >  But the reason for eliminating the probe-sets with
 > the highest variability is less clear for me.

Perhaps you misunderstood the below example code, it only eliminates 
low-variability probesets and keeps the high-variability ones. Please 
give it a second look.

Best wishes
   Wolfgang

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Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

Boel Brynedal ha scritto:
> 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