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_MONETAR Y=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 -- MFT?Services University?of?Tuebingen Calwerstr.?7 72076??T?bingen/GERMANY Tel.:?+49?(0)?7071?29?83210 Fax.?+?49?(0)?7071?29?5228 Confidentiality?Note: This?message?is?intended?only?for?the?use?of?the?named?recipient(s)?an d?may contain?confidential?and/or?proprietary?information.?If?you?are?not?th e?intended recipient,?please?contact?the?sender?and?delete?the?message.?Any?unaut horized use?of?the?information?contained?in?this?message?is?prohibited

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_MONET ARY=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

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) > > -----Urspr?ngliche 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_MON ETARY=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 > -- MFT?Services University?of?Tuebingen Calwerstr.?7 72076??T?bingen/GERMANY Tel.:?+49?(0)?7071?29?83210 Fax.?+?49?(0)?7071?29?5228 Confidentiality?Note: This?message?is?intended?only?for?the?use?of?the?named?recipient(s)?an d?may contain?confidential?and/or?proprietary?information.?If?you?are?not?th e?intended recipient,?please?contact?the?sender?and?delete?the?message.?Any?unaut horized use?of?the?information?contained?in?this?message?is?prohibited

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@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_MONET ARY=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

Hi Philip, Thank you very much. Sometimes things are as simple as that. Kind regards, Michael > -----Urspr?ngliche Nachricht----- > Von: "Groot, Philip de" <philip.degroot at="" wur.nl=""> > Gesendet: 17.11.09 11:42:32 > 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 > 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_MON ETARY=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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- MFT?Services University?of?Tuebingen Calwerstr.?7 72076??T?bingen/GERMANY Tel.:?+49?(0)?7071?29?83210 Fax.?+?49?(0)?7071?29?5228 Confidentiality?Note: This?message?is?intended?only?for?the?use?of?the?named?recipient(s)?an d?may contain?confidential?and/or?proprietary?information.?If?you?are?not?th e?intended recipient,?please?contact?the?sender?and?delete?the?message.?Any?unaut horized use?of?the?information?contained?in?this?message?is?prohibited