Hi all
I reply in this thread because I also have the "could not locate a
file" problem which I cannot solve.
My code:
setwd("/x05/people/m140932/eclipse/workspace/CNV"); # here I set the
working directory
library("aroma.affymetrix");
log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE);
options(digits=4);
stopifnot(isDirectory("annotationData"));
stopifnot(isDirectory("annotationData/chipTypes"));
stopifnot(isDirectory("annotationData/chipTypes/GenomeWideSNP_6"));
stopifnot(isFile("annotationData/chipTypes/GenomeWideSNP_6/
GenomeWideSNP_6,Full.cdf"));
cdf <- AffymetrixCdfFile$byChipType("GemomeWideSNP_6", tags="Full");
My paths and files:
>pwd
/x05/people/m140932/eclipse/workspace/CNV/annotationData/chipTypes/
GenomeWideSNP_6
>ll
total 673949
-rw-r--r-- 1 scicomp 493291745 2009-09-01 16:49
GenomeWideSNP_6,Full.cdf
-rw-r--r-- 1 scicomp 7526454 2009-09-02 07:54
GenomeWideSNP_6,Full,na26,HB20080722.ufl
-rw-r--r-- 1 scicomp 9407937 2009-09-02 07:55
GenomeWideSNP_6,Full,na26,HB20080821.ugp
-rw-r--r-- 1 scicomp 179217531 2009-09-02 08:03
GenomeWideSNP_6,HB20080710.acs
I checked many times the paths and filenames but cannot see the error.
I still get the following error message:
Error in list(`AffymetrixCdfFile$byChipType("GemomeWideSNP_6", tags =
"Full")` = <environment>, :
[2009-09-02 09:09:17] Exception: Could not locate a file for this chip
type: GemomeWideSNP_6,Full
at throw(Exception(...))
at throw.default("Could not locate a file for this chip type: ",
paste(c(chipT
at throw("Could not locate a file for this chip type: ", paste(c
(chipType, tag
at method(static, ...)
at AffymetrixCdfFile$byChipType("GemomeWideSNP_6", tags = "Full")
I am using R2.9.1 on Linux (with the Eclipse StatET plug-in).
Thanks for your help
cheers
Jerome
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