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stage.R
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stage.R
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## working through the links Vineet provided to download, unzip, convert to expression data for the 6 datasets, then save as a .csv
## sometimes when I it it tells me that one study or another doesnt have supplemental files, but if I run it again I'll usually get them?
##I havent yet included the clinical data from each study
##one issue I am still having/ having to work through is an error I get for GSE1456 ---
## Error in read.celfile.probeintensity.matrices(filenames = filenames, cdfInfo = cdfInfo, :
## Cel file C:/Users/Dan/Documents/GSE1456_data/GSM107232.CEL does not seem to be of HG-U133A type
##I guess the .cel files are of different types and the function I found only runs on one of those types? Looking at them on NCBI, indeed half of them are HG-U133B
library(GEOquery)
library(affy)
datasets <- c('./data/GSE2034','./data/GSE1456','./data/GSE2990','./data/GSE4922','./data/GSE7390','./data/GSE11121')
for (i in datasets){
getGEOSuppFiles(i)
FP <- paste(i,"/",i,"_RAW.tar",sep="")
untar(FP, exdir=paste(i,"_data/",sep=""))
FP <- paste(i,"_data/",sep="")
cels <- list.files(FP, pattern="[gz]")
FP <- paste(i, "_data/", cels, sep="")
sapply(FP, gunzip)
}
for (i in datasets){
setwd(paste("./",i,"_data",sep=""))
eset <- justRMA()
write.csv(eset, paste(i,".csv",sep=""))
setwd("..")
}