[BioC] how presence p-values can be accessed in mas5call output?

[Martin Morgan]

"James W. MacDonald" <jmacdon at med.umich.edu> writes:

> Hi Vladimir,
>
> Vladimir Morozov wrote:
>> Hi,
>> 
>> mas5calls.AffyBatch is supposed to calulate prence p-vales:
>> "The 'mas5calls' method for 'AffyBatch' returns an 'exprSet' with
>>      calls in the 'exprs' slot and p-values in the 'se.exprs'. The
>>      code{mas5calls} for 'ProbeSet' returns a list with vectors of
>>      calls and pvalues."
>> 
>> Here is what I get from mas5call
>> 
>>>dim(exprs(ab.mas5calls))
>> 
>> [1] 45101   157
>> 
>>>exprs(ab.mas5calls)[1:2,1:3]
>> 
>>            139102 139103 139104
>> 1415670_at "P"    "P"    "P"
>> 1415671_at "P"    "P"    "P"
>> 
>> it is Ok
>> 
>> 
>>>dim(se.exprs(ab.mas5calls))
>> 
>> Error in function (classes, fdef, mtable)  :
>>     unable to find an inherited method for function "se.exprs", for
>> signature "ExpressionSet"
>
> Yeah, it looks like there isn't an accessor function for this slot for 
> ExpressionSets. However, you can get the data directly:
>
> get("se.exprs", ab.mas5calls at assayData)

Use

> assayData(ab.mas5calls)[["se.exprs"]]

instead. This uses the 'assayData' accessor to retrieve the assay
data, and the '[[' subsetting function to select the 'se.exprs'
element. Using the accessor provides some protection should the slot
name change. Using '[[' provides some protection against assayData
returning a 'list', which it is allowed to do.

Martin

>
> Best,
>
> Jim
>
>
>
>> 
>> 
>> Any suggestions how presence p-values can be accessed
>> 
>> Thnaks
>> Vladimir
>> 
>> 	[[alternative HTML version deleted]]
>> 
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>
>
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
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>
>
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-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org