[BioC] simpleAffy QC on HT_HG-U133_Plus_PM

[Groot, Philip de]

Hello all,
 
You cannot apply the simpleaffy QC function on PM plates! The MAS5 normalization procedure, which underlies the calculations, cannot handle NA in the MM probes. Consequenly, MAS5 normalization is not possible and hence QC is not possible.
 
You can use the library xps to do a "MAS5-like" approach including p-values and P/M/A calls. Additionally, you can still make many other QC plots AND apply the RMA normalization (which uses pm-probes only).
 
Regards,
 
Dr. Philip de Groot Ph.D.
Bioinformatics Researcher

Wageningen University / TIFN
Nutrigenomics Consortium
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
PO Box 8129, 6700 EV Wageningen
Visiting Address: Erfelijkheidsleer: De Valk, Building 304
Dreijenweg 2, 6703 HA  Wageningen
Room: 0052a
T: +31-317-485786
F: +31-317-483342
E-mail:   Philip.deGroot at wur.nl <mailto:Philip.deGroot at wur.nl> 
Internet: http://www.nutrigenomicsconsortium.nl <http://www.nutrigenomicsconsortium.nl/> 
             http://humannutrition.wur.nl <http://humannutrition.wur.nl/> 
             https://madmax.bioinformatics.nl <https://madmax.bioinformatics.nl/> 
 
 
 

________________________________

From: James W. MacDonald [mailto:jmacdon at med.umich.edu]
Sent: Mon 16-11-2009 18:52
To: Michael Walter
Cc: bioconductor at stat.math.ethz.ch
Subject: 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