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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