Entering edit mode
Christopher N Barnes
▴
10
@christopher-n-barnes-3179
Last seen 10.3 years ago
All,
I am new to xps and am having trouble reading in the cel files.
I got the 3 correct files from affymetrix and created a scheme
removing the first 12 lines from the annotation file (fix 1)
I then read in my scheme:
hgu133plus2<-root.scheme(paste(.path.package("xps"),"schemes/hgu133plu
s2.root",
sep="/"))
and then try to read in the CEL files.
celdir2<-"C:/McMasters/test"
data.test3<-import.data(hgu133plus2,"tmp2",celdir=celdir2,
verbose=FALSE)
It worked 1 time and now causes R to crash. I am trying to read in 40
CEL files 50,000+ genes on a 4G machine.
Does anyone have any suggestions of another method to read a large
amount of CEL files. If I try using Read Affy() to read in, I don't
have the space to allocate.
Thanks for the Help,
Chris Barnes
PhD student
University of Louisville
[[alternative HTML version deleted]]