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