[BioC] simpleAffy QC on HT_HG-U133_Plus_PM
James W. MacDonald
jmacdon at med.umich.edu
Mon Nov 16 18:52:30 CET 2009
Michael Walter wrote:
> 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)
What do you get if you do a traceback() at this point?
This looks like you are getting the error 'NAs in external function
call' (assuming that is what Funktionsaufruf means), which would
indicate to me that the problem is in the justMAS() function. Does
justMAS(data) work for you?
As an aside, 'data' isn't a really good variable name, as there is
already a data() function, so you are relying on R to figure out whether
you want to use the function or the AffyBatch of that name.
> So I'd would highly appreciate any hints, where to look for my mistake.
> Thank you very much.
> Kind regards,
> R version 2.9.0 (2009-04-17)
> attached base packages:
>  stats graphics grDevices utils datasets methods base
> other attached packages:
>  hthgu133pluspmcdf_2.4.0 geneplotter_1.22.0 annotate_1.22.0
>  AnnotationDbi_1.6.1 affyQCReport_1.22.0 lattice_0.17-26
>  RColorBrewer_1.0-2 affyPLM_1.20.0 preprocessCore_1.6.0
>  xtable_1.5-6 simpleaffy_2.20.0 gcrma_2.16.0
>  Biostrings_2.12.10 IRanges_1.2.3 genefilter_1.24.3
>  affy_1.22.1 Biobase_2.4.1
> loaded via a namespace (and not attached):
>  affyio_1.12.0 DBI_0.2-4 grid_2.9.0 RSQLite_0.7-3
>  splines_2.9.0 survival_2.35-7 tools_2.9.0
James W. MacDonald, M.S.
University of Michigan
Department of Human Genetics
1241 E. Catherine St.
Ann Arbor MI 48109-5618
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