Entering edit mode
When using the straightforward "ReadAffy()" syntax to read Affy
arrays, I am experiencing an exception which is being thrown when the
reader hits HU133B file in a particular GEO dataset. Is there an
optimal way to read Hu-133A arrays separately from HU-133B arrays
(.CEL files) from an untarred GEO data set?
Thus, far, I am attempting a workaround by generating a filename list
during untarring, and then attempting to read CEL files separately,
using:
dirname="C:/Data/GEOBreastHu133Plus/GSE1456/"
setwd(dirname)
rawcelfilename<-"C:/Data/GEOBreastHu133Plus/GSE1456/GSE1456_RAW.TAR"
untar(rawcelfilename)
filelist<-untar(rawcelfilename,list=TRUE)
for (file in filelist) {
result <- try(ReadAffy(filenames=file));
if(class(result) != "try-error"){
# data<- data + ??? <-- NEED to build up data set here after
successfully opening each HU133A (B) CEL file
}
}
If an exception is thrown due to an HU133B array, I want to go to the
next filename. The trick is also how to build up a data set based on
the successfully read CEL files -- and the above is not working.
Later on, once "data" are read, I can use:
pset <- fitPLM(data)
NUSE(pset,main="GSE1456")
eset<- rma(data)
write.exprs(eset,file="data.txt")
save(eset, file = paste("GSE1456",".RData"))
FYI, I have successfully used:
data<- ReadAffy()
for HU133Plus2.0 CEL files and have had no problem; however, the
Hu133B in this particular GEO set (1456) results in a thrown exception
since HU133A arrays are not readable in ReadAFfy by default.
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