[BioC] Extracting pvals for PA calls in affy

[Hassane, Duane]

Hi Kartik,

At the R prompt, try:
?mas5calls

The help page shows that mas5calls returns an exprSet object with p-values in the se.exprs slot

If you really want to do present call filtering as you describe, just off the top of my head, you might try:

(1) Extracting pvalues from the object resulting from mas5calls, e.g. mas5calls.out:

pvals<-mas5calls.out at se.exprs

(2) Create a function to determine the Fisher pvals that accepts a vector of the call p-values as input ... look at GeneMeta and the vignette "Meta analysis for microarrays" for instructions/code for how this might be accomplished.  I call it "yourmeta" below.  Maybe someone else can help you out here.
 
(3) Apply the function to each row of "raw" pvals to generate a vector of cumulative pvalues for each probeset:

fisherpvals<-apply(pvals,1,yourmeta)

(4) Filter by rows for which the cumulative pvalues are less than 0.05.

filtered.data<-exprs(alldata)[fisherpvals < 0.05,] 

Assuming your exprSet is named "alldata"

Is that what you wanted?  I don't know much about GeneMeta, it might contain something like "yourmeta" already.  I wish I could be more helpful right now, but this should get you started.

Best,

Duane Hassane 



-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Kartik Pappu
Sent: Thursday, August 17, 2006 7:29 PM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Extracting pvals for PA calls in affy


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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-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Kartik Pappu
Sent: Thursday, August 17, 2006 7:29 PM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Extracting pvals for PA calls in affy


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

_______________________________________________
Bioconductor mailing list
Bioconductor at stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor