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

[Martin Morgan]

Yes, sorry, the documentation is not adequate. I added assayData to
ExpressionSet (pointing toward eSet, where the method is actually
defined), and a little information to the eSet and AssayData
documentation to indicate one way of getting the elements. While on
the eSet page I was reminded of assayDataElement and
assayDataElementNames, which provides a different ways of finding out
about and manipulating the contents of assayData.

Martin

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

> 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
>
>
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org