Problem with setQCEnvironment
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@melissa-morine-2682
Last seen 10.5 years ago
Hi, I'm attempting to create a custom .qcdef file, as I am running QC on a custom affy chip. I have created the following file (named 'nugomm1a520177cdf.qcdef'): array nugomm1a520177cdf 0.05 0.065 bioB AFFX-r2-Ec-bioB-3_at bioC AFFX-r2-Ec-bioC-3_at bioD AFFX-r2-Ec-bioD-3_at creX AFFX-r2-P1-cre-3_at actin3/actin5 AFFX-b-ActinMur/M12481_3_at AFFX-b-ActinMur/M12481_5_at actin3/actinM AFFX-b-ActinMur/M12481_3_at AFFX-b-ActinMur/M12481_M_at gapdh3/gapdh5 AFFX-GapdhMur/M32599_3_at AFFX-GapdhMur/M32599_5_at gapdh3/gapdhM AFFX-GapdhMur/M32599_3_at AFFX-GapdhMur/M32599_M_at I saved this file in the directory with my .cel files. When I tried to run the setQCEnvironment command I received the following error message: >setQCEnvironment("nugomm1a520177cdf", path="/users/melissamorine/Microarray Data/CLA Data") Warning message: In readLines(fl) : incomplete final line found on '/users/melissamorine/Microarray Data/CLA Data/nugomm1a520177cdf.qcdef' I also tried adding 'spk' and 'ratio' to the beginning of the lines in the .qcdef file, as specified in the simleaffy vignette example, but that didn't make any difference. Thanks in advance for any suggestions, Melissa > sessionInfo() R version 2.6.2 (2008-02-08) i386-apple-darwin8.10.1 locale: en_IE.UTF-8/en_IE.UTF-8/en_IE.UTF-8/C/en_IE.UTF-8/en_IE.UTF-8 attached base packages: [1] splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] affyQCReport_1.16.0 geneplotter_1.16.0 lattice_0.17-4 [4] annotate_1.16.1 AnnotationDbi_1.0.6 RSQLite_0.6-4 [7] DBI_0.2-4 RColorBrewer_1.0-2 affyPLM_1.14.0 [10] xtable_1.5-2 outliers_0.13-2 simpleaffy_2.14.05 [13] gcrma_2.10.0 genefilter_1.16.0 survival_2.34 [16] car_1.2-7 nugomm1a520177cdf_1.0.4 matchprobes_1.10.0 [19] affy_1.16.0 preprocessCore_1.0.0 affyio_1.6.1 [22] Biobase_1.16.1 loaded via a namespace (and not attached): [1] KernSmooth_2.22-22 grid_2.6.2 [3] mmnugomm1a520177mmentrezg_10.0.0
cdf affy cdf affy • 1.1k views
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@james-w-macdonald-5106
Last seen 1 day ago
United States
Hi Melissa, You got a warning, not an error (the difference being that R said 'Hmmm, that doesn't seem right.' rather than saying 'ERRRRRR crash boom thud!'). In other words, things should have worked anyway. Did they not? Anyway, the problem here is that you didn't add a final carriage return when you created the .qcdef file. From ?readLines warn: logical. Warn if a text file is missing a final EOL. Where EOL is (apparently obviously) an End Of Line character, which you create by hitting the Enter key. Best, Jim Melissa Morine wrote: > Hi, > > I'm attempting to create a custom .qcdef file, as I am running QC on a > custom affy chip. > > I have created the following file (named 'nugomm1a520177cdf.qcdef'): > > array nugomm1a520177cdf > 0.05 > 0.065 > bioB AFFX-r2-Ec-bioB-3_at > bioC AFFX-r2-Ec-bioC-3_at > bioD AFFX-r2-Ec-bioD-3_at > creX AFFX-r2-P1-cre-3_at > actin3/actin5 AFFX-b-ActinMur/M12481_3_at AFFX-b-ActinMur/M12481_5_at > actin3/actinM AFFX-b-ActinMur/M12481_3_at AFFX-b-ActinMur/M12481_M_at > gapdh3/gapdh5 AFFX-GapdhMur/M32599_3_at AFFX-GapdhMur/M32599_5_at > gapdh3/gapdhM AFFX-GapdhMur/M32599_3_at AFFX-GapdhMur/M32599_M_at > > > > I saved this file in the directory with my .cel files. > > When I tried to run the setQCEnvironment command I received the > following error message: > >> setQCEnvironment("nugomm1a520177cdf", > path="/users/melissamorine/Microarray Data/CLA Data") > > Warning message: > In readLines(fl) : > incomplete final line found on '/users/melissamorine/Microarray > Data/CLA Data/nugomm1a520177cdf.qcdef' > > I also tried adding 'spk' and 'ratio' to the beginning of the lines in > the .qcdef file, as specified in the simleaffy vignette example, but > that didn't make any difference. > > Thanks in advance for any suggestions, > Melissa > >> sessionInfo() > R version 2.6.2 (2008-02-08) > i386-apple-darwin8.10.1 > > locale: > en_IE.UTF-8/en_IE.UTF-8/en_IE.UTF-8/C/en_IE.UTF-8/en_IE.UTF-8 > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] affyQCReport_1.16.0 geneplotter_1.16.0 lattice_0.17-4 > [4] annotate_1.16.1 AnnotationDbi_1.0.6 RSQLite_0.6-4 > [7] DBI_0.2-4 RColorBrewer_1.0-2 affyPLM_1.14.0 > [10] xtable_1.5-2 outliers_0.13-2 simpleaffy_2.14.05 > [13] gcrma_2.10.0 genefilter_1.16.0 survival_2.34 > [16] car_1.2-7 nugomm1a520177cdf_1.0.4 matchprobes_1.10.0 > [19] affy_1.16.0 preprocessCore_1.0.0 affyio_1.6.1 > [22] Biobase_1.16.1 > > loaded via a namespace (and not attached): > [1] KernSmooth_2.22-22 grid_2.6.2 > [3] mmnugomm1a520177mmentrezg_10.0.0 > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
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Hi, Thanks for the reply James. I tried adding a carriage return to the last line, but unfortunately I'm still having the same problem with my .qcdef file. I do just get a warning message after executing the setQCEnvironment command, but I get a proper error message when I try and run the QC: Error in setQCEnvironment(cdfn) : Could not find array definition file ' nugomm1a520177cdf.qcdef '. Simpleaffy does not know the QC parameters for this array type. See the package vignette for details about how to specify QC parameters manually. In addition: Warning message: closing unused connection 3 (/users/melissamorine/Microarray Data/CLA Data/nugomm1a520177cdf.qcdef) Hmmm, any other suggestions? Thanks very much, Melissa ----- Original Message ----- From: "James W. MacDonald" <jmacdon@med.umich.edu> Date: Thursday, February 28, 2008 2:31 pm Subject: Re: [BioC] Problem with setQCEnvironment To: Melissa Morine <melissa.morine at="" ucd.ie=""> Cc: bioconductor at stat.math.ethz.ch > Hi Melissa, > > You got a warning, not an error (the difference being that R said > 'Hmmm, > that doesn't seem right.' rather than saying 'ERRRRRR crash boom > thud!'). > In other words, things should have worked anyway. Did they not? > > Anyway, the problem here is that you didn't add a final carriage > return > when you created the .qcdef file. From ?readLines > > warn: logical. Warn if a text file is missing a final EOL. > > Where EOL is (apparently obviously) an End Of Line character, which > you > create by hitting the Enter key. > > Best, > > Jim > > > > Melissa Morine wrote: > > Hi, > > > > I'm attempting to create a custom .qcdef file, as I am running QC > on a > > custom affy chip. > > > > I have created the following file (named 'nugomm1a520177cdf.qcdef'): > > > > array nugomm1a520177cdf > > 0.05 > > 0.065 > > bioB AFFX-r2-Ec-bioB-3_at > > bioC AFFX-r2-Ec-bioC-3_at > > bioD AFFX-r2-Ec-bioD-3_at > > creX AFFX-r2-P1-cre-3_at > > actin3/actin5 AFFX-b-ActinMur/M12481_3_at AFFX-b- > ActinMur/M12481_5_at> actin3/actinM AFFX-b-ActinMur/M12481_3_at > AFFX-b-ActinMur/M12481_M_at > > gapdh3/gapdh5 AFFX-GapdhMur/M32599_3_at AFFX-GapdhMur/M32599_5_at > > gapdh3/gapdhM AFFX-GapdhMur/M32599_3_at AFFX-GapdhMur/M32599_M_at > > > > > > > > I saved this file in the directory with my .cel files. > > > > When I tried to run the setQCEnvironment command I received the > > following error message: > > > >> setQCEnvironment("nugomm1a520177cdf", > > path="/users/melissamorine/Microarray Data/CLA Data") > > > > Warning message: > > In readLines(fl) : > > incomplete final line found on '/users/melissamorine/Microarray > > Data/CLA Data/nugomm1a520177cdf.qcdef' > > > > I also tried adding 'spk' and 'ratio' to the beginning of the > lines in > > the .qcdef file, as specified in the simleaffy vignette example, but > > that didn't make any difference. > > > > Thanks in advance for any suggestions, > > Melissa > > > >> sessionInfo() > > R version 2.6.2 (2008-02-08) > > i386-apple-darwin8.10.1 > > > > locale: > > en_IE.UTF-8/en_IE.UTF-8/en_IE.UTF-8/C/en_IE.UTF-8/en_IE.UTF-8 > > > > attached base packages: > > [1] splines tools stats graphics grDevices utils > datasets> methods base > > > > other attached packages: > > [1] affyQCReport_1.16.0 geneplotter_1.16.0 lattice_0.17- > 4 > > [4] annotate_1.16.1 AnnotationDbi_1.0.6 RSQLite_0.6- > 4 > > [7] DBI_0.2-4 RColorBrewer_1.0-2 > affyPLM_1.14.0 > > [10] xtable_1.5-2 outliers_0.13-2 > simpleaffy_2.14.05 > > [13] gcrma_2.10.0 genefilter_1.16.0 > survival_2.34 > > [16] car_1.2-7 nugomm1a520177cdf_1.0.4 > matchprobes_1.10.0 > > [19] affy_1.16.0 preprocessCore_1.0.0 affyio_1.6.1 > > > [22] Biobase_1.16.1 > > > > loaded via a namespace (and not attached): > > [1] KernSmooth_2.22-22 grid_2.6.2 > > > [3] mmnugomm1a520177mmentrezg_10.0.0 > > > > _______________________________________________ > > 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 > -- > James W. MacDonald, M.S. > Biostatistician > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 >
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Ok, I just figured out the problem with my .qcdef file. After unsuccessfully trying all combinations of spaces, identifiers and carriage returns, I re-opened the file using the R editor, saved it from there and ran the setQCEnvironment function with no problems! I probably should've known that the Mac TextEditor program would cause problems. I claim ignorance due to being a new Mac user... Btw, the format I ended up using for the .qcdef file was the same as the one in the simpleaffy vignette (and the one James sent me. Thanks!) Melissa ----- Original Message ----- From: Melissa Morine <melissa.morine@ucd.ie> Date: Thursday, February 28, 2008 4:48 pm Subject: Re: [BioC] Problem with setQCEnvironment To: bioconductor at stat.math.ethz.ch > Hi, > > Thanks for the reply James. > > I tried adding a carriage return to the last line, but > unfortunately I'm > still having the same problem with my .qcdef file. I do just get a > warning message after executing the setQCEnvironment command, but I > geta proper error message when I try and run the QC: > > Error in setQCEnvironment(cdfn) : > Could not find array definition file ' nugomm1a520177cdf.qcdef '. > Simpleaffy does not know the QC parameters for this array type. > See the package vignette for details about how to specify QC > parametersmanually. > In addition: Warning message: > closing unused connection 3 (/users/melissamorine/Microarray Data/CLA > Data/nugomm1a520177cdf.qcdef) > > > Hmmm, any other suggestions? > > Thanks very much, > Melissa > > ----- Original Message ----- > From: "James W. MacDonald" <jmacdon at="" med.umich.edu=""> > Date: Thursday, February 28, 2008 2:31 pm > Subject: Re: [BioC] Problem with setQCEnvironment > To: Melissa Morine <melissa.morine at="" ucd.ie=""> > Cc: bioconductor at stat.math.ethz.ch > > > Hi Melissa, > > > > You got a warning, not an error (the difference being that R said > > 'Hmmm, > > that doesn't seem right.' rather than saying 'ERRRRRR crash boom > > thud!'). > > In other words, things should have worked anyway. Did they not? > > > > Anyway, the problem here is that you didn't add a final carriage > > return > > when you created the .qcdef file. From ?readLines > > > > warn: logical. Warn if a text file is missing a final EOL. > > > > Where EOL is (apparently obviously) an End Of Line character, > which > > you > > create by hitting the Enter key. > > > > Best, > > > > Jim > > > > > > > > Melissa Morine wrote: > > > Hi, > > > > > > I'm attempting to create a custom .qcdef file, as I am running > QC > > on a > > > custom affy chip. > > > > > > I have created the following file (named > 'nugomm1a520177cdf.qcdef'):> > > > > array nugomm1a520177cdf > > > 0.05 > > > 0.065 > > > bioB AFFX-r2-Ec-bioB-3_at > > > bioC AFFX-r2-Ec-bioC-3_at > > > bioD AFFX-r2-Ec-bioD-3_at > > > creX AFFX-r2-P1-cre-3_at > > > actin3/actin5 AFFX-b-ActinMur/M12481_3_at AFFX-b- > > ActinMur/M12481_5_at> actin3/actinM AFFX-b-ActinMur/M12481_3_at > > AFFX-b-ActinMur/M12481_M_at > > > gapdh3/gapdh5 AFFX-GapdhMur/M32599_3_at AFFX- GapdhMur/M32599_5_at > > > gapdh3/gapdhM AFFX-GapdhMur/M32599_3_at AFFX- GapdhMur/M32599_M_at > > > > > > > > > > > > I saved this file in the directory with my .cel files. > > > > > > When I tried to run the setQCEnvironment command I received the > > > following error message: > > > > > >> setQCEnvironment("nugomm1a520177cdf", > > > path="/users/melissamorine/Microarray Data/CLA Data") > > > > > > Warning message: > > > In readLines(fl) : > > > incomplete final line found on '/users/melissamorine/Microarray > > > Data/CLA Data/nugomm1a520177cdf.qcdef' > > > > > > I also tried adding 'spk' and 'ratio' to the beginning of the > > lines in > > > the .qcdef file, as specified in the simleaffy vignette > example, but > > > that didn't make any difference. > > > > > > Thanks in advance for any suggestions, > > > Melissa > > > > > >> sessionInfo() > > > R version 2.6.2 (2008-02-08) > > > i386-apple-darwin8.10.1 > > > > > > locale: > > > en_IE.UTF-8/en_IE.UTF-8/en_IE.UTF-8/C/en_IE.UTF-8/en_IE.UTF-8 > > > > > > attached base packages: > > > [1] splines tools stats graphics grDevices utils > > datasets> methods base > > > > > > other attached packages: > > > [1] affyQCReport_1.16.0 geneplotter_1.16.0 > lattice_0.17- > > 4 > > > [4] annotate_1.16.1 AnnotationDbi_1.0.6 > RSQLite_0.6- > > 4 > > > [7] DBI_0.2-4 RColorBrewer_1.0-2 > > affyPLM_1.14.0 > > > [10] xtable_1.5-2 outliers_0.13-2 > > simpleaffy_2.14.05 > > > [13] gcrma_2.10.0 genefilter_1.16.0 > > survival_2.34 > > > [16] car_1.2-7 nugomm1a520177cdf_1.0.4 > > matchprobes_1.10.0 > > > [19] affy_1.16.0 preprocessCore_1.0.0 > affyio_1.6.1 > > > > > [22] Biobase_1.16.1 > > > > > > loaded via a namespace (and not attached): > > > [1] KernSmooth_2.22-22 grid_2.6.2 > > > > > > [3] mmnugomm1a520177mmentrezg_10.0.0 > > > > > > _______________________________________________ > > > 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 > > -- > > James W. MacDonald, M.S. > > Biostatistician > > Affymetrix and cDNA Microarray Core > > University of Michigan Cancer Center > > 1500 E. Medical Center Drive > > 7410 CCGC > > Ann Arbor MI 48109 > > 734-647-5623 > > > > _______________________________________________ > 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
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