[BioC] simpleAffy QC on HT_HG-U133_Plus_PM
Michael Walter
michael.walter at med.uni-tuebingen.de
Mon Nov 16 16:37:31 CET 2009
Dear all,
I'm trying to use the simpleAffy QC functions to look at some HT_HG-U133_Plus_PM arrays which are not recognized automatically. So I followed the vignette and created a config file which looks like follows:
array hthgu133pluspmcdf
alpha1 0.05
alpha2 0.065
spk bioB AFFX-r2-Ec-bioB-3_at
spk bioC AFFX-r2-Ec-bioC-3_at
spk bioD AFFX-r2-Ec-bioD-3_at
spk creX AFFX-r2-P1-cre-3_at
ratio actin3/actin5 AFFX-HSAC07/X00351_3_at AFFX-HSAC07/X00351_5_at
ratio actin3/actinM AFFX-HSAC07/X00351_3_at AFFX-HSAC07/X00351_M_at
ratio gapdh3/gapdh5 AFFX-HUMGAPDH/M33197_3_at AFFX-HUMGAPDH/M33197_5_at
ratio gapdh3/gapdhM AFFX-HUMGAPDH/M33197_3_at AFFX-HUMGAPDH/M33197_M_at
I save the file as "hthgu133pluspmcdf.qcdef in the same folder as all the default config files.
When I try to analyse the Affy batch I get following error message:
>data <- ReadAffy(celfile.path=celfile, filenames=filenames)
>path2QCenv = "C:/Programme/R/R-2.9.0/library/simpleaffy/extdata"
>setQCEnvironment(cleancdfname(cdfName(data)),path2QCenv)
>qc.cel <- qc(data)
Fehler: NAs in externem Funktionsaufruf (arg 1)
So I'd would highly appreciate any hints, where to look for my mistake.
Thank you very much.
Kind regards,
Michael
> sessionInfo()
R version 2.9.0 (2009-04-17)
i386-pc-mingw32
locale:
LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] hthgu133pluspmcdf_2.4.0 geneplotter_1.22.0 annotate_1.22.0
[4] AnnotationDbi_1.6.1 affyQCReport_1.22.0 lattice_0.17-26
[7] RColorBrewer_1.0-2 affyPLM_1.20.0 preprocessCore_1.6.0
[10] xtable_1.5-6 simpleaffy_2.20.0 gcrma_2.16.0
[13] Biostrings_2.12.10 IRanges_1.2.3 genefilter_1.24.3
[16] affy_1.22.1 Biobase_2.4.1
loaded via a namespace (and not attached):
[1] affyio_1.12.0 DBI_0.2-4 grid_2.9.0 RSQLite_0.7-3
[5] splines_2.9.0 survival_2.35-7 tools_2.9.0
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