I am trying to make a csv file to do some machine learning in WEKA, the data set I want to use is GSE31799. I have used the following lines of code with other data sets with out a problem (For example GSE2109).
I have downloaded the .CEL files into a folder extracted them and created a phenodata file.
celfiles <- read.affy(covdesc="phenodata.txt") celfiles.gcrma <-gcrma(celfiles) eset<-exprs(celfiles.gcrma) Transposed <- t(eset) write.csv(Transposed, file="GSE31799_gcrma.csv", append= FALSE, row.names=TRUE, col.names=TRUE)
However I get the following error when executing the second line:
Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.15 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain RM-HU01Aa520485 Library - package rmhu01aa520485cdf not installed Bioconductor - rmhu01aa520485cdf not available
I think I have a cdf file that goes with this data set (rmhu01aa520485.cdf)
But i can't work out how to use it?