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

[cstrato]

Dear Luis,

The annotation file "HuGene-1_1-st-v1.na30.hg19.probeset.csv" contains 
probesets which are not present in the pgf-file. For this reason 
Affymetrix has updated the file to 
"HuGene-1_1-st-v1.na30.1.hg19.probeset.csv". Could you please use this 
annotation file.
(Files "HuGene-1_1-st-v1.na30.hg19.transcript.csv" and 
"HuGene-1_0-st-v1.na30.hg19.transcript.csv" should be identical.)

If you still have problems could you please use Rterm with verbose=TRUE 
and send me the complete output.

Best regards
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
_._._._._._._._._._._._._._._._._._



Luis Campos wrote:
> 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
>
>