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

[James W. MacDonald]

Hi Martin,

Martin Morgan wrote:
> 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.

Is this in lieu of an se.exprs() accessor? If so it might be worthwhile 
to add something to the ExpressionSet-class help page. I don't see 
anything there for the assayData() accessor itself, nor anything about 
how one might subset the output from this accessor safely.

Best,

Jim


> 
> Martin

-- 
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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