[BioC] Extracting pvals for PA calls in affy

[Kartik Pappu]

Hi all,

I am new to using bioconductor.  I was wondering if there was a way to
extract the p-values that are used to make the P/M/A calls when one
runs the "mas5calls" function in affy.

Secondly,  I am wondering if someone has already come up with a
solution for the bigger problem I am facing.  I have data from 6 affy
chips (3 expt and 3 control).  what I want to be able to do is get rid
of all the probe sets that are called absent in both sets.  I have
seen a report that uses the Fisher test on pvalues (that are used to
make the A/M/P calls) and come up with a cumulative pvalue (which
follows a chi square distribution).  Then "If the combined p-value for
a given probe set is greater than a cutoff (0.05) for both control and
experiment (i.e. called "absent" in both samples), then the probe set
is filtered out".

This is exactly what I want to do with my data. Any sugggestions on
how to do this?

Thanks Much
Kartik