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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