Hi Christian,

I am trying to do an analysis using xps and the hugene11 chip. However, I run into problems for which I need your help.

I created a small test-script to demonstrate the problem:

library(xps)
scheme <- root.scheme("/local2/R-2.15.2/library/xps/schemes/hugene11stv1.root")
x.xps <- import.data(scheme, "tmp_x", celdir = ".", celfiles = "G092_A05_01_1.1.CEL", verbose = TRUE)

cat("The loaded .CEL-files are:\n");
for (i in 1:length(rawCELName(x.xps, fullpath = FALSE)))
  cat(sprintf("%s\n", rawCELName(x.xps, fullpath = FALSE)[i]));

Upon execution, I get:
> library(xps)

Welcome to xps version 1.18.1
    an R wrapper for XPS - eXpression Profiling System
    (c) Copyright 2001-2012 by Christian Stratowa

> scheme <- root.scheme("/local2/R-2.15.2/library/xps/schemes/hugene11stv1.root")
> x.xps <- import.data(scheme, "tmp_x", celdir = ".", celfiles = "G092_A05_01_1.1.CEL", verbose = TRUE)
Opening file </local2/R-2.15.2/library/xps/schemes/hugene11stv1.root> in <READ> mode...
Creating new temporary file </mnt/geninf16/home/guests/pdegroot/dataanalysis/PHILIPG/tmp_x_cel.root>...
Importing <./G092_A05_01_1.1.CEL> as <G092_A05_01_1.1.cel>...
   hybridization statistics:
      1 cells with minimal intensity 19
      1 cells with maximal intensity 21364.4
New dataset <DataSet> is added to Content...
>
> cat("The loaded .CEL-files are:\n");
The loaded .CEL-files are:
> for (i in 1:length(rawCELName(x.xps, fullpath = FALSE)))
+   cat(sprintf("%s\n", rawCELName(x.xps, fullpath = FALSE)[i]));
Error: Tree set <> could not be found in file content
Error: Tree set <> could not be found in file content
NA

The weird thing is: I only have this problem with the hugene11 chip. As far as I can see, al other chips work properly (still na32 based).
This effects all other steps, because there is no "content" to normalise etc.

I created the root-scheme as follows:
scmdir <- paste(.path.package("xps"), "schemes/", sep = "/")
scheme <- import.exon.scheme("hugene11stv1",filedir=scmdir, layoutfile=paste(libdir, "HuGene-1_1-st-v1.r4.clf", sep="/"), schemefile=paste(libdir,"HuGene-1_1-st-v1.r4.pgf", sep="/"), probeset=paste(anndir,"HuGene-1_1-st-v1.na33.1.hg19.probeset.csv", sep="/"), transcript=paste(anndir,"HuGene-1_1-st-v1.na33.1.hg19.transcript.csv", sep="/"), add.mask = TRUE)

(libdir and anndir are also defined off course).

I even updated the na32 annotation to the latest Affymetrix version (na33) the exclude a problem there. It does not fix the issue.
Please note that I am running root version 5.32/04 as version 5.32/01 is no longer available for download. Root works properly as far as I can see.

Do you have any clue where this problem originates from? Thank you!

sessionInfo():
> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] xps_1.18.1

loaded via a namespace (and not attached):
[1] tools_2.15.2

Regards,

Dr. Philip de Groot
Bioinformatician / Microarray analysis expert

Wageningen University / TIFN
Netherlands Nutrigenomics Center (NNC)
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
PO Box 8129, 6700 EV Wageningen
Visiting Address:
"De Valk" ("Erfelijkheidsleer"),
Building 304,
Verbindingsweg 4, 6703 HC Wageningen
Room: 0052a
T: 0317 485786
F: 0317 483342
E-mail: Philip.deGroot@wur.nl<mailto:Philip.deGroot@wur.nl>
I:         http://humannutrition.wur.nl<http://humannutrition.wur.nl/>
           https://madmax.bioinformatics.nl
           http://www.nutrigenomicsconsortium.nl<http://www.nutrigenomicsconsortium.nl/>




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