[BioC] Simpleaffy Error: the following are not valid files
Boel Brynedal
Boel.Brynedal at ki.se
Tue Apr 15 13:56:02 CEST 2008
Dear List,
I am trying to perform a simple pairwise comparison in simpleaffy, which
I have done before, but something goes wrong at the first step.
> rawP<-read.affy()
Error: the following are not valid files:
./'BB52.CEL'
./'BB46.CEL'
./'BB58.CEL'
# (complete list of CEL-files in directory)
#The covdesc-file is there and looks ok:
> covdesc[1:2,]
Disease specific Boels_ID Tissue Gender LabDate
BB52.CEL MS MS_rem 03-104_PBL PBL Male 02/08/2007
BB46.CEL MS MS_rem 03-017_PBL PBL Male 02/08/2007
> sessionInfo()
R version 2.6.0 (2007-10-03)
x86_64-unknown-linux-gnu
locale:
.....
attached base packages:
[1] splines tools stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] simpleaffy_2.14.05 gcrma_2.10.0 matchprobes_1.10.0
[4] genefilter_1.16.0 survival_2.34-1 affy_1.16.0
[7] preprocessCore_1.0.0 affyio_1.6.1 Biobase_1.16.3
loaded via a namespace (and not attached):
[1] annotate_1.16.1 AnnotationDbi_1.0.6 DBI_0.2-4
[4] rcompgen_0.1-17 RSQLite_0.6-8
I don't understand where it has gone wrong, I've done this before
without any trouble. Have I made a apperent misstake? I am wondering a
bit about the "./" before every CEL-file name in the error message....
Any tips will be appreciated!
Best,
Boel
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