[BioC] Problems with expresso

[Martin Morgan]

Hi Markus --

Try providing an argument for pmcorrect.method, as in
example(expresso).

My hint toward this was

> showMethods("computeExprSet")
Function: computeExprSet (package affy)
x="AffyBatch", pmcorrect.method="character", summary.method="character"

This says that computeExprSet has a method defined when
pmcorrect.method is of type character, whereas the error message (and
glancing at the arguments of expresso) suggest that pmcorrect.method
is NULL by default.

Martin


Markus Schmidberger <schmidb at ibe.med.uni-muenchen.de> writes:

> Hello,
>
> I want to use expresso for preprocessing the hgu133a-spikein data from 
> affycompII. But there is an error:
>
>  > library(affy)
>  > path <- "z:/Microarray/hgu133a-spikein/rawdata"
>  > celFile <- list.celfiles(path=path,full.names=TRUE);
>  > affyBatch <- ReadAffy(filenames=celFile[1:6]);
>  > eset1 <- 
> expresso(affyBatch,bgcorrect.method="rma",normalize.method="quantiles",summary.method="medianpolish") 
>
> background correction: rma
> normalization: quantiles
> PM/MM correction :
> expression values: medianpolish
> background correcting...done.
> normalizing...done.
> Fehler in function (classes, fdef, mtable)  :
>        unable to find an inherited method for function "computeExprSet", 
> for signature "AffyBatch", "NULL", "character"
>
>
> ALL packages are up to date, first of all I did a update:
> ## *new* R session, no saved data loaded
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("Biobase")
>> library("Biobase")
>> update.packages(repos=biocReposList())
>
>
>  > sessionInfo()
> 2.5.1 (2007-06-27)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252
>
> attached base packages:
> [1] "tools"     "stats"     "graphics"  "grDevices" "utils"     
> "datasets"  "methods"   "base"    
>
> other attached packages:
> hgu133atagcdf          affy        affyio       Biobase
>      "1.16.0"      "1.14.2"       "1.4.1"      "1.14.1"
>
> Whats wrong? The function "computeExprSet" exists in library(affy)
>
> Thanks
> Markus
>
> -- 
> Dipl.-Tech. Math. Markus Schmidberger
>
> Ludwig-Maximilians-Universität München
> IBE - Institut für medizinische Informationsverarbeitung,
> Biometrie und Epidemiologie
> Marchioninistr. 15, D-81377 Muenchen
> URL: http://ibe.web.med.uni-muenchen.de 
> Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de
>
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-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org