All:
This is probably a newbe rookie question but I am trying to iterate through a list (matrix?) and it fails with:
"Error in gsedf[i, 1] : object of type 'S4' is not subsettable"
This is strange because I have another script which works perfectly with almost the same code. I am using GEOquery to extract the list of GSM files that makeup a GSE set. The gsedf is a list of GSE files to download and process. This works in my other script but fails with the error message above in the script below. I don't know if this is really due to iterating through the list or to processing each GSM file from the GSE set to extract the data table. The script does process the first GSE accession in the list, just it fails apparently when it starts on the second GSE accession in the list. I have re-ordered the list and it processes the first GSE in the list but fails with the same error before going on to the second. Thanks for any help.
Code follows:
#!/usr/bin/Rscript
library("GEOquery")
library("Biobase")
#options(warn = 1)
# get the filename of GSE numbers as argument
args = commandArgs(trailingOnly = TRUE)
# assign filename to f
f = args[1]
f
# read in the table of filenames
gselist <- list(read.table(f, header=FALSE, sep="", quote=""));
gselist
# make a dataframe from gselist
gsedf <- data.frame(gselist)
gsedf
y=nrow(gsedf)
print(paste("GSElist Length", y))
#this works perfectly to see if it was an iteration problem
for(i in 1:y){
gsename <- gsedf[i,]
print(paste("gsename=",gsename,sep=""))
}
# This is the part that fails
# iterate through each GSE
for (i in 1:y){
gsename <- gsedf[i,1]
print(paste("GSEno=",i,"Name=",gsename))
# get the gds object
gsedf<-getGEO(gsename, GSEMatrix=FALSE, destdir=".")
gsmnamesdf<-data.frame(names(GSMList(gsedf))) #get list of sample names
#and make a data frame
gsefile=paste(gsename, "-samples.txt", sep="")#make output file name for sample
#list
print("Writing Samplename file")
write.table(gsmnamesdf, file=gsefile, sep="\t") #write list of samples
z=nrow(gsmnamesdf) #get number of sample names
print(paste("Number of Samples=",z))
for (j in 1:z){ #iterate through each sample name
print(paste("SampleNum=",j,sep=""))
gsm = gsmnamesdf[j,] #sample name of j sample
print(paste("Sample Name=",gsm))
gsmdf <- getGEO(gsm, destdir=".") #get sample
outfile=paste(gsm,"table.txt",sep="-")#make sample output file name
tabledf <- Table(gsmdf)#extract data table from the GSM accession
print(paste("Printing",outfile))
write.table(tabledf, file=outfile, sep="\t")#write the table to file
# clean up
softfile=paste(gsm,".soft", sep="")# the softfile name
gzfile=paste(gsename, ".soft.gz", sep=" ")# the zippped softfile name
print(paste("Deleting",softfile, sep=" "))
file.remove(softfile) #delete the soft file
file.remove(gzfile) #delete the zipped file
}
}
print("Ended processing")
q()
