[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"
>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, 


> sessionInfo()
R version 2.9.0 (2009-04-17) 


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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