[BioC] Advise on setting up a non-specific filter for differential expression

[Tobias Straub]

Hi Lucia

I am not sure if I completely understand your problem, just want to mention that I routinely apply non-specific filtering based on MAS5 calls with a very good outcome (based on a prior-knowledge training set). I do not like so much the alternative approach - filtering based on variance or IQR -  as it jeopardizes my preferred way of defining responders by applying a threshold on the local false discovery rate.

Could you extend a bit on how you exactly filter based on MAS5 calls, how you define responders and non-responders in qPCR, how your "FDR disaster" exactly looks like.

What is your model system by the way, which arrays you use?

best regards
T.


On Aug 13, 2010, at 7:11 PM, Lucia Peixoto wrote:

> Dear All,
> I want to set up a non-specific filter to eliminate genes that are juts not
> expressed from further statistical analysis. I've previously tried a filter
> based on Mas5 presence/absence calls which turned out to be a disaster for
> the FDR (as measured by lots of qPCRs), probably because 1/3 of the MM
> probes actually hybridize better than PM, who knows.
> 
> In any case, my plan is to set up a filter based both on raw fluorescent
> intensity and IQR. I am trying to get as much sensitivity as possible
> without increasing my FDR too much.
> I was thinking that using the intensity distributions and box plots of the
> raw data may be useful to determine what the best cutoffs to obtain the best
> sensitivity will be.
> Any advise on how to select appropriate cutoffs?
> 
> Thank you very much in advance
> Lucia
> 
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Dr. Tobias Straub ++4989218075439 Adolf-Butenandt-Institute, München D