Dear Christian,
 
I am new to XPS and i would like to use it to analyse Mouse Gene ST
arrays (MoGene ST arrays). However, XPS crashes my R session when trying
to create a ROOT scheme file fore these arrays, and i don't know what
may go wrong. Hopefully you can advise. :)
 
Thanks,
Guido
 
 
What did i do?
- I am using a windows machine (WinXP-SP3, 4GB memory)
- I installed ROOT v5.24.00 (1st) and XPS (2nd). PS: is there a way to
check whether ROOT installed properly?
- Then i downloaded the 'library' files', MoGene-1_0-st-v1.r4.pgf and
MoGene-1_0-st-v1.r4.clf, and put them in a directory
(D:\XPS\Affy\libraryfiles)
- Next i downloaded the latest annotation files from Affymetrix
(MoGene-1_0-st-v1.na29.mm9.transcript.csv and
MoGene-1_0-st-v1.na29.mm9.probeset.csv), and repaired them according to
your instructions here:
http://article.gmane.org/gmane.science.biology.informatics.conductor/245
87. The annotation files are in the dir D:\XPS\Affy\Annotation.
- I also created a dir to save the ROOT scheme file
(D:\XPS\CRAN\Workspaces\Schemes).
 
When running XPS to create the scheme file R crashes...
 
My lines of code:
library(xps)
libdir <- "d:/XPS/Affy/libraryfiles"
anndir <- "d:/XPS/Affy/Annotation"
scmdir <- "d:/XPS/CRAN/Workspaces/Schemes"

Below it crashes (line is from your previous referred post on the
mailing list):
 
scheme.mogene10stv1r4.na29 <- 
import.exon.scheme("Scheme_MoGene10stv1r4_na29",filedir=scmdir,
paste(libdir,"MoGene-1_0-st-v1.r4.clf",sep="/"), 
paste(libdir,"MoGene-1_0-st-v1.r4.pgf",sep="/"), 
paste(anndir,"MoGene-1_0-st-v1.na29.mm9.probeset.fixed.csv",sep="/"),
paste(anndir,"MoGene-1_0-st-v1.na29.mm9.transcript.fixed.csv",sep="/"))
 
Error message:
Rgui.exe - Application error. The instruction at "0x002288931"
references memory at "0x8d5056fc". The memory could not be "read".
 

> sessionInfo()
R version 2.9.0 (2009-04-17) 
i386-pc-mingw32 
 
locale:
LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
Kingdom.1252;LC_MONETARY=English_United
Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
 
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

 
other attached packages:
[1] xps_1.4.8
> 
 
 
 

------------------------------------------------ 
Guido Hooiveld, PhD 
Nutrition, Metabolism & Genomics Group 
Division of Human Nutrition 
Wageningen University 
Biotechnion, Bomenweg 2 
NL-6703 HD Wageningen 
the Netherlands 
tel: (+)31 317 485788 
fax: (+)31 317 483342 
internet:   http://nutrigene.4t.com <http://nutrigene.4t.com/>  
email:      guido.hooiveld@wur.nl 



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