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"
sessionInfo()
R version 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
______________________________________________
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
