[BioC] Cannot read in CEL files with XPS

cstrato cstrato at aon.at
Thu Dec 4 22:38:40 CET 2008

Dear Chris

This is strange, could you please give your sessionInfo(), which version 
of xps,  which version of ROOT, which version of R, WinXP or Vista?

Could you please give the complete code for creating the scheme.
I am not sure if it is a good idea to save the "hgu133plu2.root" file in 
the package directory, I would propose to create a directory "schemes" 
somewhere else, e.g. "McMasters/schemes".

Furthermore, could you please set "verbose=TRUE" in the methods and 
start R from the Command Console. Then you will see the progress 
messages. Could you please send me this output, so that I can check the 

Handling 40 CEL-files should not be a problem, one user of xps reported 
that he could successfully handle 500 CEL-files on his Windows machine.

Best regards
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at

Christopher N Barnes wrote:
> 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/hgu133plus2.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]]
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