[BioC] Extracting pvals for PA calls in affy

[Jenny Drnevich]

Hi Kartik,

I use a simpler method to remove absent probesets. If a probeset has at 
least 1 'present' call or at least 2 'marginal' calls, then I keep it , 
otherwise I throw it out. This may not be as sophisticated as what you want 
to do, but it will remove almost all of the probesets you want to remove. 
Here's a piece of code I use to convert the P/M/A calls to numbers:

calls.eset <- mas5calls(rawdata)

num.pres <- apply(exprs(calls.eset), 1, function(x) {
         x[x == "A"] <- 0
         x[x == "P"] <- 1
         x[x == "M"] <- 0.3
         x <- as.numeric(x)
         return(sum(x))
     })

You can change the valuation of the M calls, but I use 0.3 to distinguish 2 
Marginal from 1 Present. Then, you can subset an exprSet object using 
whatever numerical cutoff you want:

eset.pres <- eset.all[num.pres > 0.5 , ]


Cheers,
Jenny



At 07:28 PM 8/17/2006, Kartik Pappu wrote:
>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
>
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
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e-mail: drnevich at uiuc.edu