Hi, use full.names=TRUE in your list.files call to get the full path to your files. J. On 06/14/2011 06:54 PM, array chip wrote: > I figured it out, I need to start R session in the directory where the cel files > are stored. > > > > > ________________________________ > > To: bioconductor at r-project.org > Sent: Tue, June 14, 2011 9:41:05 AM > Subject: [BioC] CEL files not valid? > > Hi I downloaded GSE2034 dataset from GEO. But when I tried to read in these cel > files using ReadAffy(), I got the following error message: > >> library(affy) >> fls<-list.files("my directory to CEL files", ".*cel")## get cell files >> aBatch<-ReadAffy(filenames=fls)## input raw CEL files > Error: the following are not valid files: > GSM177885.cel > GSM177886.cel > GSM177887.cel > GSM177888.cel > : > : > > Anyone has any suggestions what is going on? > >> sessionInfo() > R version 2.12.2 (2011-02-25) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C LC_TIME=English_United States.1252 > > > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] affy_1.28.1 Biobase_2.10.0 rcom_2.2-3.1 rscproxy_1.3-1 > > loaded via a namespace (and not attached): > [1] affyio_1.18.0 preprocessCore_1.12.0 tools_2.12.2 > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >