[BioC] problem with creating array annotation package

[cstrato]

Dear Guido,

In principle you could use package xps for the analysis of CHO arrays. 
It uses the clf/pgf-files and annotation files from Affymetrix.

To create a 'scheme' file for xps you can for example do:

library(xps)

libdir <- "/Volumes/GigaDrive/Affy/libraryfiles"
anndir <- "/Volumes/GigaDrive/Affy/Annotation"
scmdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes"

# CHOGene-2_0-st: used as exon array
scheme.chogene20st <- import.exon.scheme("chogene20st", filedir = 
file.path(scmdir, "na33"),
    file.path(libdir, "CHOGene-2_0-st.clf"),
    file.path(libdir, "CHOGene-2_0-st.pgf"),
    file.path(anndir, "Version13Mar", 
"CHOGene-2_0-st-v1.na33.2.crigri1.probeset.csv"),
    file.path(anndir, "Version13Mar", 
"CHOGene-2_0-st-v1.na33.2.crigri1.transcript.csv"))

Best regards,
Christian
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