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

Martin Morgan mtmorgan at fhcrc.org
Tue Jun 12 21:44:54 CEST 2007

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.


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

> Hi Martin,
> Martin Morgan wrote:
>> Use
>> 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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Martin Morgan
Bioconductor / Computational Biology

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