[BioC] How to use detect call in GCRMA (or RMA) analysis?

[Amit Bahl]

If you have a PM-only array, the mas5calls function will not do.   
I've seen a couple of ad hoc strategies for calling P/A only from PM  
probes, but never accompanied with comparison to MAS5 or some other  
quality metric.  Has anyone dealt with this problem?

-Amit

On Dec 7, 2006, at 8:21 AM, Jianping Jin wrote:

> You may want to try "mas5calls", a function in the affy package and  
> then
> filter out the probesets with most absent calls.
> For example:
>
> PAcalls <- mas5calls(affybatch.obj)
>
> HTH,
>
> JP-
>
> --On Wednesday, December 06, 2006 10:47 PM +0000 Wang mingyi
> <mingyiwang at hotmail.com> wrote:
>
>> Dear all,
>>
>> I have a question for Affymetrix data analysis by GCRMA (or RMA).  
>> From
>> the GCRMA (RMA) results, we cannot get detect call information  
>> which can
>> be returned from MAS5. I think this information are useful when we  
>> want
>> to perform some downstream t-tests. For example, three replicates  
>> (after
>> drug) comparing with other three replicates (before drug), if  
>> given one
>> gene, most detect values are "A" in all these 6 replicates, we  
>> will think
>> the t-test doesnot make sense. So how to deal with this situation?  
>> Can we
>> incorporate with detect call information from MAS5?
>> Thank you in advance!
>>
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>
>
>
> ##################################
> Jianping Jin Ph.D.
> Bioinformatics scientist
> Center for Bioinformatics
> Room 3133 Bioinformatics building
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> Chapel Hill, NC 27599
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> FAX:   (919)843-3103
> E-Mail: jjin at email.unc.edu
>
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