[BioC] XPS: Human Gene 1.0 ST v1 Summarization using Affy Library r4

[Luis Campos]

Hi,

I have run into an error that I cannot quite figure out. I want to run a
summarization on the Human Gene 1.0 ST v1 chip using the XPS package and
using the 4th revision of the library (r4). I have looked through the
mailing list and cannot seem to find someone who had the same problem.

Since r4 is now essentially an exon scheme i used import.exon.scheme as
mentioned in the help files as follows:

  >  library(xps)
Welcome to xps version 1.6.4
      an R wrapper for XPS - eXpression Profiling System
      (c) Copyright 2001-2009 by Christian Stratowa

*(it was suggested to use the entire directory when inserting the file
name as below)
*(since I m on a Windows XP machine, I have also tried: paste, "\\"
instead of "/")
  >  scheme.hugene10stv1r4.na30 = import.exon.scheme(filename   =
"HuGene_10_st_v1",
                     filedir    = "G:/APT/XPS",
                     layoutfile = "G:/APT/Affy_lib/HuGene-1_0-st-v1.r4.clf",
                     schemefile = "G:/APT/Affy_lib/HuGene-1_0-st-v1.r4.pgf",
                     probeset   =
"G:/APT/Affy_lib/HuGene-1_0-st-v1.na30.hg19.probeset.csv",
                     transcript =
"G:/APT/Affy_lib/HuGene-1_0-st-v1.na30.hg19.transcript.csv",
                     add.mask   = FALSE,
                     verbose    = TRUE)
I get the following Error:
      Error in import.exon.scheme(filename = "HuGene_10_st_v1", filedir =
"G:/APT/XPS",  :
    error in function 'ImportExonSchemes'

(I checked the error value and it is (-13))

***It was mentioned in the help page for import.exon.scheme thata ",
since Affymetrix is still changing the headers and/or columns of the
annotation files, future annotation files may require adaptation of the
source code, thus the current version of 'xps' may not be able to read
these files."***
If this is the case, since I have the most updated version of the
Annotation and library files, could this be the problem?

Also, in the internal 'ImportExonSchemes' function the error that is
occuring has the non-zero value of -13, this may help.Thank you very
much in advance.


Here is my Session Info:

>  sessionInfo()
R version 2.10.1 (2009-12-14)
i386-pc-mingw32

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_UnitedStates.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_1.6.4



~Luis Campos


-- 
Luis Campos
Junior Specialist
Division of Biostatistics
Public Health Sciences, UC Davis
530-752-4046