[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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