[BioC] Package "xps" import.data error

[cstrato]

Dear Yonghong

Since you are using xps with Windows I suppose that you are using RGui.

In order to get more information about your problem may I suggest to run 
xps using RTerm with verbose=TRUE. This will show you more information 
and give you a hint about the concrete problem, see:
https://www.stat.math.ethz.ch/pipermail/bioconductor/2008-December/025452.html

Could you please send me the complete output from RTerm.

Could you also please update to a newer version of xps, xps_1.0.2 is 
pretty old.

Maybe, one last note: From your code I assume that you have imported the 
exon scheme in the same R session as the CEL-files. Since the pgf and 
annotation files consume huge amounts of memory it is better to import 
the exon scheme in a separate R session first. When starting a new R 
session you can use "root.scheme()" to import the created scheme and 
import the CEL-files in the new R session.

Please let me know if this could solve your problem, otherwise please 
send me the output from RTerm, as already mentioned.

Best regards
Christian
_._._._._._._._._._._._._._._._._._
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
_._._._._._._._._._._._._._._._._._



Wang, Yonghong (NIH/NCI) [C] wrote:
> Hello all:
>
> I am new to XPS package and would like to use it to perform affymetrix
> EXON array data analysis. Basically I copied and paseted the sample
> codes and ran the analysis. Originally, I tried some test dataset (cel
> files) and works fine. But when I ran my cel files, I got the error
> message. Basically I can't import the Cel files into R package. The code
> I was using is listed below. I am using window system with R version
> 2.8.1. I am thinking that the error might be caused by some kinds of
> incompatibilities, but can't prove it. Any helps would be very
> appreciated.
>
> Best
>
> Yonghong
>
>  
>
> Code:
>
>  
>
>   
>> setwd("c:/R_file")
>>     
>
>   
>> library(xps)
>>     
>
>  
>
> Welcome to xps version 1.0.2 
>
>     an R wrapper for XPS - eXpression Profiling System
>
>     (c) Copyright 2001-2008 by Christian Stratowa
>
>     
>
>   
>> homedir <- "c:/R_file/"
>>     
>
>   
>> libdir <- paste(homedir, "libraryfiles", sep="")
>>     
>
>   
>> anndir <- paste(homedir, "Annotation", sep="")
>>     
>
>   
>> scmdir <- paste(homedir, "CRAN/Workspaces/Schemes", sep="")
>>     
>
>   
>> celdir <- paste(homedir, "CEL", sep="")
>>     
>
>   
>> datdir <- paste(homedir, "ROOTData", sep="")
>>     
>
>   
>> tmpdir <- paste(homedir, "CRAN/Workspaces/Exon/temp", sep="")
>>     
>
>   
>> celfiles <- c("H2452.CEL", "H2596.CEL")
>>     
>
>   
>> celnames <- substring(celfiles,1)
>>     
>
>   
>> scheme.huex10stv2r2.na27f <-
>>     
> import.exon.scheme("Scheme_HuEx10stv2r2_na27f",filedir=scmdir,
>
> +
> layoutfile=paste(libdir,"HuEx-1_0-st-v2.r2.clf",sep="/"),
>
> +
> schemefile=paste(libdir,"HuEx-1_0-st-v2.r2.pgf",sep="/"),
>
> +
> probeset=paste(anndir,"HuEx-1_0-st-v2.na27.hg18.probeset.csv",sep="/"),
>
> +
> transcript=paste(anndir,"HuEx-1_0-st-v2.na27.hg18.transcript.csv",sep="/
> "))
>
>   
>> scheme.exon
>>     
> <-root.scheme(paste(scmdir,"Scheme_HuEx10stv2r2_na27f.root",sep="/"))
>
>   
>> test.data<- import.data(scheme.exon, "test_data",filedir = datdir,
>>     
> celdir = celdir, celfiles = celfiles, verbose = FALSE)
>
> Error in import.data(scheme.exon, "test_data", filedir = datdir, celdir
> = celdir,  : 
>
>   error in function 'ImportData'
>
>   
>
>
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>
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