Dear list,

I need to do a batch effect removal on  a few batches of Affymetrix Human Gene 1.0 ST arrays by using Evan Johnson's ComBat script. Since the input file for ComBat requires detection call information, I decide to use dabg.call () in xps package for the calculation (Human Gene 1.0 ST array doesn't have MM probes). I download the following chip definition and annotation files from Affymetrix web site: Unsupported Human Gene 1.0 ST Array CDF Files (zip, 13 MB), HuGene-1_0-st-v1 Probe Sequences, tabular format (21 MB, 2/23/10), HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 31 (10 MB, 9/3/10), unzip them and put them into respective directories. Then I get the "Error in import.expr.scheme..." message when trying to import chip definition and annotation files to a ROOT scheme. I notice an early post about the similar error (https://stat.ethz.ch/pipermail/bioconductor/2008-October/024718.html) and follow the direction to remove the header in
 annotation file. However the error still exists. Could anyone shed me some light on solving this problem? 

Thanks a lot.

Lei



> library(xps)

Welcome to xps version 1.8.3 
    an R wrapper for XPS - eXpression Profiling System
    (c) Copyright 2001-2010 by Christian Stratowa
    
> libdir <- "C:/mypath/Affy/library"
> anndir <- "C:/mypath/Affy/annotation"
> scmdir <- "C:/mypath/CRAN/Workspaces/Schemes"

> scheme.hugene.1.0.st <- import.expr.scheme("Scheme_HuGene_1_0_st_v1.na31", filedir=scmdir,
+                        schemefile=paste(libdir, "HuGene-1_0-st-v1.r3.cdf", sep="/"),
+                        probefile=paste(libdir, "HuGene-1_0-st-v1.hg19.probe.tab", sep="/"),
+                        annotfile=paste(anndir, "HuGene-1_0-st-v1.na31.hg19.annot.csv", sep="/"),
+                        verbose=TRUE)
Error in import.expr.scheme("Scheme_HuGene_1_0_st_v1.na31", filedir = scmdir,  : 
  error in function ‘ImportExprSchemes’
> sessionInfo()
R version 2.11.1 (2010-05-31) 
i386-pc-mingw32 

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] xps_1.8.3       R2HTML_2.1      svSocket_0.9-48 svIDE_0.9-49   

loaded via a namespace (and not attached):
[1] svMisc_0.9-60 tcltk_2.11.1  tools_2.11.1  XML_3.2-0.1  
> 




      
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