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

[James W. MacDonald]

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)


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
Ann Arbor MI 48109
734-647-5623


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