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Hi BioC,
I am having problems getting ReadAffy to work on fc5. Any ideas?
Thanks.
Aedin
> example(ReadAffy)
RdAffy> if(require(affydata)){
RdAffy+ celpath <- system.file("celfiles", package="affydata")
RdAffy+ fns <- list.celfiles(path=celpath,full.names=TRUE)
RdAffy+
RdAffy+ cat("Reading files:\n",paste(fns,collapse="\n"),"\n")
RdAffy+ ##read a binary celfile
RdAffy+ abatch <- ReadAffy(filenames=fns[1])
RdAffy+ ##read a text celfile
RdAffy+ abatch <- ReadAffy(filenames=fns[2])
RdAffy+ ##read all files in that dir
RdAffy+ abatch <- ReadAffy(celfile.path=celpath)
RdAffy+ }
Loading required package: affydata
Reading files:
/home/aedin/R/i686-redhat-linux-gnu-
library/2.5/affydata/celfiles/binary.cel
/home/aedin/R/i686-redhat-linux-gnu-
library/2.5/affydata/celfiles/text.cel
Error in read.affybatch(filenames = l$filenames, phenoData =
l$phenoData, :
VECTOR_ELT() can only be applied to a 'list', not a 'char'
> sessionInfo()
R version 2.5.0 (2007-04-23)
i686-redhat-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US
.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGE
S=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE
=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFI
CATION=C
attached base packages:
[1] "tools" "stats" "graphics" "grDevices" "utils"
"datasets"
[7] "methods" "base"
other attached packages:
affydata affy affyio Biobase
"1.11.2" "1.14.1" "1.0.0" "1.14.0"