[BioC] se.exprs extractor question

[Richard Pearson]

Kellie

I think this was discussed on this list very recently ("how presence 
p-values can be accessed in mas5call output?"). Anyhow, try the following:

assayDataElement(PACalls,"se.exprs")[1:10,]

Regards

Richard.


Kellie J. Archer, Ph.D. wrote:
> I am wanting to directly use the p-values estimated from mas5calls, 
> and following the example,
>
> > data(affybatch.example)
> > PACalls <- mas5calls(affybatch.example)
> Getting probe level data...
> Computing p-values
> Making P/M/A Calls
> > se.exprs(PACalls)[1:10,]
> Error in function (classes, fdef, mtable)  :
>        unable to find an inherited method for function "se.exprs", for 
> signature "ExpressionSet"
>
> In previous releases the p-values were stored in se.exprs, and the 
> help still indicates that is the case. Does anyone know how they can 
> be extracted?
> > sessionInfo()
> R version 2.5.0 (2007-04-23)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
> States.1252;LC_MONETARY=English_United 
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] "tools"     "stats"     "graphics"  "grDevices" "utils"     
> "datasets"
> [7] "methods"   "base"   
> other attached packages:
>    affy   affyio  Biobase
> "1.14.1"  "1.4.0" "1.14.0"
>
> -Kellie Archer
> ------------------------------------------------------------------------
>
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