Search
Question: CEL files not valid?
0
gravatar for array chip
6.0 years ago by
array chip340
array chip340 wrote:
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]]
ADD COMMENTlink modified 6.0 years ago • written 6.0 years ago by array chip340
0
gravatar for array chip
6.0 years ago by
array chip340
array chip340 wrote:
I figured it out, I need to start R session in the directory where the cel files are stored. ________________________________ To: bioconductor@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@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]]
ADD COMMENTlink written 6.0 years ago by array chip340
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 >
ADD REPLYlink written 6.0 years ago by James F. Reid610
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 258 users visited in the last hour