[BioC] Affy PA calls

[Mark Cowley]

hi Loren,
the way i use P/M/A calls is to exclude probesets that are absent in all samples. This usually filters out 30-50% of the genes that are not expressed in your samples. Then let maanova/limma/SAM find the differentially expressed genes on those genes detected in at least one sample.

If you really want to pursue your PA call idea, then you can calculate how many present calls there are in each group, and find genes that have 3 P's vs 0 P's in the 2 groups & vice versa:

calls <- mas5calls( .... )
calls <- exprs(calls)
Pcount.duroc <- apply(calls[,1:3] == "P", 1, sum)
Pcount.york <- apply(calls[,4:6] == "P", 1, sum)

HTH
Mark

On 30/07/2010, at 10:37 AM, Sean Davis wrote:

> On Thu, Jul 29, 2010 at 8:28 PM, Loren Engrav <engrav at u.washington.edu>wrote:
> 
>> 
>> Sorry if was too terse
>> 
>> I have Affy chips from shallow and deep wounds in 3 Duroc and 3 Yorkshire
>> pigs. And I have the p-values from maanova and q-values from Storey
>> q-values
>> which returned 171 probes of interest.
>> 
>> I would also like the 3 Durocs and the 3 Yorkshire bio reps to be the
>> "same".
>> 
>> So the general question is how to define "same"?
>> 
>> The specific question is can the Affy PA calls be used to define same?  If
>> one pig is PA meaning shallow is Present and deep is Absent, can I say the
>> other two pigs should also be PA?  Or is the PA call too suspect to be used
>> in this way?
>> 
>> 
> That is a pretty blunt instrument.
> 
> Doesn't your hypothesis test define sameness, at least relative to the other
> group?  Again, you may need to elaborate a bit more on what you are doing.
> 
> Sean
> 
> 
> 
>>> From: Mark Cowley <m.cowley at garvan.org.au>
>>> Date: Fri, 30 Jul 2010 10:02:56 +1000
>>> To: Loren Engrav <engrav at u.washington.edu>
>>> Cc: rbioc <bioconductor at stat.math.ethz.ch>
>>> Subject: Re: [BioC] Affy PA calls
>>> 
>>> hi Loren,
>>> please elaborate
>>> mark
>>> 
>>> On 30/07/2010, at 8:55 AM, Loren Engrav wrote:
>>> 
>>>> Does anyone put much stock in Affy PA calls?
>>>> 
>>>> I searched gmane and I think the answer is No. True?
>>>> 
>>>> Thank you.
>>>> 
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>>> 
>> 
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