[Bioc-devel] pval in mas5calls()

[Martin Morgan]

Christian:

The values are there, just not accessible with se.exprs. Try
'assayData(obj)[["se.exprs"]]':

> example(mas5calls)

ms5cll> data(affybatch.example)

ms5cll> PACalls <- mas5calls(affybatch.example)
Getting probe level data...
Computing p-values
Making P/M/A Calls
> dim(assayData(PACalls)[["se.exprs"]])
[1] 150   3

Martin

cstrato <cstrato at aon.at> writes:

> Dear all,
>
> Could it be that function mas5calls() no longer returns the p-values, 
> since se.exprs does no longer exist?
>
> I get:
> pr.call <- mas5calls(pr)
> call <-exprs(pr.call)
> pval <-se.exprs(pr.call) ||
> Error in function (classes, fdef, mtable)  :
>         unable to find an inherited method for function "se.exprs", for 
> signature "ExpressionSet"
>
> Interestingly, the source code in "mas5.R" still creates an 
> ExpressionSet with "se.exprs=p".
>
> sessionInfo()
> R version 2.5.0 (2007-04-23)
> i386-apple-darwin8.9.1
>
> locale:
> C
>
> attached base packages:
> [1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"
> [7] "methods"   "base"    
>
> other attached packages:
> hgu95av2cdf        affy      affyio     Biobase
>    "1.16.0"    "1.14.0"     "1.4.0"    "1.14.0"
>
> Best regards
> Christian
>
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-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org