[BioC] simpleAffy QC on HT_HG-U133_Plus_PM

Michael Walter michael.walter at med.uni-tuebingen.de
Tue Nov 17 09:06:39 CET 2009


Hi Jim,

Thanks for your help and sorry for the german error message. Anyway, your guess was right. When I call the traceback() function I get this output (which doesn't tell me much to be honest). When I use justMAS(data) I get the same error message as with qc(data). Is it a problem of the target value?

Kind regards, 

Michael


> traceback()
7: .C("bgmas", as.integer(as.vector(all)), as.integer(length(all)), 
       as.double(as.vector(this.array)), as.integer(length(this.array)), 
       as.integer(rws), as.integer(cls), as.integer(grid[1]), as.integer(grid[2]), 
       zonebg = double(grid[1] * grid[2]), zonesd = double(grid[1] * 
           grid[2]), corrected = double(length(this.array)), PACKAGE = "simpleaffy")
6: bg.correct.sa(unnormalised)
5: justMAS(x, tgt = sc)
4: call.exprs(unnormalised, "mas5")
3: qc.affy(unnormalised, ...)
2: qc(data)
1: qc(data)


> 

> -----Ursprüngliche Nachricht-----
> Von: "James W. MacDonald" <jmacdon at med.umich.edu>
> Gesendet: 16.11.09 18:53:14
> An: Michael Walter <michael.walter at med.uni-tuebingen.de>
> CC: bioconductor at stat.math.ethz.ch
> Betreff: Re: [BioC] simpleAffy QC on HT_HG-U133_Plus_PM


> Hi Michael,
> 
> 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"
> >> setQCEnvironment(cleancdfname(cdfName(data)),path2QCenv)
> >> 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.
> 
> Best,
> 
> Jim
> 
> 
> 
> > 
> > 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    
> > 
> > 
> > 
> > 
> 
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
> 

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