Human Illumina Methylation27k question
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@juan-fernandez-tajes-5273
Last seen 10.2 years ago
Dear list, It is possible to import GenomeStudio v1 data into R with lumi package? The headers in my GenomeStudio final report are these: AVG_Beta, Avg_NBEADS_A, Avg_NBEADS_B, BEAD_STDERR_A, BEAD_STDERR_B, Signal_A, Signal_B, Detection.Pval, Intensity. The code that I followed: library(lumi) fileName <- 'MET0007_1Ronda_2Ronda_FinalReport.txt' x.lumi <- lumiR.batch(fileName, columnNameGrepPattern=list(exprs='AVG_Beta', se.exprs='BEAD_STDERR', detection='Detection.Pval', beadNum='Avg_NBEADS'), inputAnnotation=F) The error that I got: Error en lumiR(file.i, parseColumnName = FALSE, convertNuID = FALSE, QC = FALSE, : Different column numbers of exprs and se.exprs! Please check the input data format. my sessionInfo(): R version 2.14.0 (2011-10-31) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] es_ES.UTF-8/es_ES.UTF-8/es_ES.UTF-8/C/es_ES.UTF-8/es_ES.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] lumi_2.6.0 nleqslv_1.9.3 methylumi_2.0.13 Biobase_2.14.0 loaded via a namespace (and not attached): [1] affy_1.32.1 affyio_1.22.0 annotate_1.32.3 AnnotationDbi_1.16.19 BiocInstaller_1.2.1 DBI_0.2-5 [7] grid_2.14.0 hdrcde_2.15 IRanges_1.12.6 KernSmooth_2.23-7 lattice_0.20-6 MASS_7.3-18 [13] Matrix_1.0-5 mgcv_1.7-14 nlme_3.1-103 preprocessCore_1.16.0 RSQLite_0.11.1 tools_2.14.0 [19] xtable_1.7-0 zlibbioc_1.0.1 Any help would be very appreciated Juan --------------------------------------------------------------- Juan Fernandez Tajes, ph. D Grupo XENOMAR Departamento de Biología Celular y Molecular Facultad de Ciencias-Universidade da Coruña Tlf. +34 981 167000 ext 2030 e-mail: jfernandezt@udc.es ---------------------------------------------------------------- [[alternative HTML version deleted]]
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@djie-tjwan-thung-5053
Last seen 10.2 years ago
Hi Juan, Try the lumiMethyR function for reading in your final report instead of using the lumiR function. I.e.: library(lumi) fileName <- 'MET0007_1Ronda_2Ronda_FinalReport.txt' x.lumi <- lumiMethyR(fileName) Good luck! Djie 2012/5/9 Juan Fernández Tajes <jfernandezt@udc.es> > Dear list, > > It is possible to import GenomeStudio v1 data into R with lumi package? > The headers in my GenomeStudio final report are these: > > AVG_Beta, Avg_NBEADS_A, Avg_NBEADS_B, BEAD_STDERR_A, BEAD_STDERR_B, > Signal_A, Signal_B, Detection.Pval, Intensity. > > The code that I followed: > > library(lumi) > fileName <- 'MET0007_1Ronda_2Ronda_FinalReport.txt' > x.lumi <- lumiR.batch(fileName, > columnNameGrepPattern=list(exprs='AVG_Beta', se.exprs='BEAD_STDERR', > detection='Detection.Pval', beadNum='Avg_NBEADS'), inputAnnotation=F) > > The error that I got: > > Error en lumiR(file.i, parseColumnName = FALSE, convertNuID = FALSE, QC = > FALSE, : > Different column numbers of exprs and se.exprs! Please check the input > data format. > > my sessionInfo(): > > R version 2.14.0 (2011-10-31) > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > locale: > [1] es_ES.UTF-8/es_ES.UTF-8/es_ES.UTF-8/C/es_ES.UTF-8/es_ES.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] lumi_2.6.0 nleqslv_1.9.3 methylumi_2.0.13 Biobase_2.14.0 > > loaded via a namespace (and not attached): > [1] affy_1.32.1 affyio_1.22.0 annotate_1.32.3 AnnotationDbi_1.16.19 > BiocInstaller_1.2.1 DBI_0.2-5 > [7] grid_2.14.0 hdrcde_2.15 IRanges_1.12.6 KernSmooth_2.23-7 > lattice_0.20-6 MASS_7.3-18 > [13] Matrix_1.0-5 mgcv_1.7-14 nlme_3.1-103 preprocessCore_1.16.0 > RSQLite_0.11.1 tools_2.14.0 > [19] xtable_1.7-0 zlibbioc_1.0.1 > > Any help would be very appreciated > > Juan > > --------------------------------------------------------------- > Juan Fernandez Tajes, ph. D > Grupo XENOMAR > Departamento de Biología Celular y Molecular > Facultad de Ciencias-Universidade da Coruña > Tlf. +34 981 167000 ext 2030 > e-mail: jfernandezt@udc.es > ---------------------------------------------------------------- > > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Hi Djie: I´ve tried but I got another error..... Error in grep(dattypes$original[i], cn) : invalid 'pattern' argument Any more ideas? Thanks a lot Juan --------------------------------------------------------------- Juan Fernandez Tajes, ph. D Grupo XENOMAR Departamento de Biología Celular y Molecular Facultad de Ciencias-Universidade da Coruña Tlf. +34 981 167000 ext 2030 e-mail: jfernandezt@udc.es ---------------------------------------------------------------- De: "Djie Tjwan Thung" <djie.thung@gmail.com> Para: "Juan Fernández Tajes" <jfernandezt@udc.es> CC: Bioconductor@r-project.org Enviados: Miércoles, 9 de Mayo 2012 13:27:55 Asunto: Re: [BioC] Human Illumina Methylation27k question Hi Juan, Try the lumiMethyR function for reading in your final report instead of using the lumiR function. I.e.: library(lumi) fileName <- 'MET0007_1Ronda_2Ronda_FinalReport.txt' x.lumi <- lumiMethyR(fileName) Good luck! Djie 2012/5/9 Juan Fernández Tajes < jfernandezt@udc.es > Dear list, It is possible to import GenomeStudio v1 data into R with lumi package? The headers in my GenomeStudio final report are these: AVG_Beta, Avg_NBEADS_A, Avg_NBEADS_B, BEAD_STDERR_A, BEAD_STDERR_B, Signal_A, Signal_B, Detection.Pval, Intensity. The code that I followed: library(lumi) fileName <- 'MET0007_1Ronda_2Ronda_FinalReport.txt' x.lumi <- lumiR.batch(fileName, columnNameGrepPattern=list(exprs='AVG_Beta', se.exprs='BEAD_STDERR', detection='Detection.Pval', beadNum='Avg_NBEADS'), inputAnnotation=F) The error that I got: Error en lumiR(file.i, parseColumnName = FALSE, convertNuID = FALSE, QC = FALSE, : Different column numbers of exprs and se.exprs! Please check the input data format. my sessionInfo(): R version 2.14.0 (2011-10-31) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] es_ES.UTF-8/es_ES.UTF-8/es_ES.UTF-8/C/es_ES.UTF-8/es_ES.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] lumi_2.6.0 nleqslv_1.9.3 methylumi_2.0.13 Biobase_2.14.0 loaded via a namespace (and not attached): [1] affy_1.32.1 affyio_1.22.0 annotate_1.32.3 AnnotationDbi_1.16.19 BiocInstaller_1.2.1 DBI_0.2-5 [7] grid_2.14.0 hdrcde_2.15 IRanges_1.12.6 KernSmooth_2.23-7 lattice_0.20-6 MASS_7.3-18 [13] Matrix_1.0-5 mgcv_1.7-14 nlme_3.1-103 preprocessCore_1.16.0 RSQLite_0.11.1 tools_2.14.0 [19] xtable_1.7-0 zlibbioc_1.0.1 Any help would be very appreciated Juan --------------------------------------------------------------- Juan Fernandez Tajes, ph. D Grupo XENOMAR Departamento de Biología Celular y Molecular Facultad de Ciencias-Universidade da Coruña Tlf. +34 981 167000 ext 2030 e-mail: jfernandezt@udc.es ---------------------------------------------------------------- [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
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Hi Juan, I'm not sure about this error, but I think it indicates that the header columns are in the wrong format. AVG_Beta, Avg_NBEADS_A, Avg_NBEADS_B, BEAD_STDERR_A, BEAD_STDERR_B, Signal_A, Signal_B, Detection.Pval, Intensity. Are you sure each of the above column names have a sample name prepended to them? I.e. sample1.AVG_Beta, sample1.Avg_NBEADS_A. After the sample name there should be a dot that seperates the sample name and column name like AVG_Beta. If your file has a format like this, then I don't know the solution and you're better off waiting for someone to reply with more knowledge than me ;). Good luck, Djie 2012/5/9 Juan Fernández Tajes <jfernandezt@udc.es> > Hi Djie: > > I´ve tried but I got another error..... > > Error in grep(dattypes$original[i], cn) : invalid 'pattern' argument > > Any more ideas? > > Thanks a lot > > > Juan > > --------------------------------------------------------------- > Juan Fernandez Tajes, ph. D > Grupo XENOMAR > Departamento de Biología Celular y Molecular > Facultad de Ciencias-Universidade da Coruña > Tlf. +34 981 167000 ext 2030 > e-mail: jfernandezt@udc.es > ---------------------------------------------------------------- > > > ------------------------------ > *De: *"Djie Tjwan Thung" <djie.thung@gmail.com> > *Para: *"Juan Fernández Tajes" <jfernandezt@udc.es> > *CC: *Bioconductor@r-project.org > *Enviados: *Miércoles, 9 de Mayo 2012 13:27:55 > *Asunto: *Re: [BioC] Human Illumina Methylation27k question > > > Hi Juan, > > Try the lumiMethyR function for reading in your final report instead of > using the lumiR function. > > I.e.: > library(lumi) > fileName <- 'MET0007_1Ronda_2Ronda_FinalReport.txt' > x.lumi <- lumiMethyR(fileName) > > Good luck! > > Djie > > > 2012/5/9 Juan Fernández Tajes <jfernandezt@udc.es> > >> Dear list, >> >> It is possible to import GenomeStudio v1 data into R with lumi package? >> The headers in my GenomeStudio final report are these: >> >> AVG_Beta, Avg_NBEADS_A, Avg_NBEADS_B, BEAD_STDERR_A, BEAD_STDERR_B, >> Signal_A, Signal_B, Detection.Pval, Intensity. >> >> The code that I followed: >> >> library(lumi) >> fileName <- 'MET0007_1Ronda_2Ronda_FinalReport.txt' >> x.lumi <- lumiR.batch(fileName, >> columnNameGrepPattern=list(exprs='AVG_Beta', se.exprs='BEAD_STDERR', >> detection='Detection.Pval', beadNum='Avg_NBEADS'), inputAnnotation=F) >> >> The error that I got: >> >> Error en lumiR(file.i, parseColumnName = FALSE, convertNuID = FALSE, QC = >> FALSE, : >> Different column numbers of exprs and se.exprs! Please check the input >> data format. >> >> my sessionInfo(): >> >> R version 2.14.0 (2011-10-31) >> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >> >> locale: >> [1] es_ES.UTF-8/es_ES.UTF-8/es_ES.UTF-8/C/es_ES.UTF-8/es_ES.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] lumi_2.6.0 nleqslv_1.9.3 methylumi_2.0.13 Biobase_2.14.0 >> >> loaded via a namespace (and not attached): >> [1] affy_1.32.1 affyio_1.22.0 annotate_1.32.3 AnnotationDbi_1.16.19 >> BiocInstaller_1.2.1 DBI_0.2-5 >> [7] grid_2.14.0 hdrcde_2.15 IRanges_1.12.6 KernSmooth_2.23-7 >> lattice_0.20-6 MASS_7.3-18 >> [13] Matrix_1.0-5 mgcv_1.7-14 nlme_3.1-103 preprocessCore_1.16.0 >> RSQLite_0.11.1 tools_2.14.0 >> [19] xtable_1.7-0 zlibbioc_1.0.1 >> >> Any help would be very appreciated >> >> Juan >> >> --------------------------------------------------------------- >> Juan Fernandez Tajes, ph. D >> Grupo XENOMAR >> Departamento de Biología Celular y Molecular >> Facultad de Ciencias-Universidade da Coruña >> Tlf. +34 981 167000 ext 2030 >> e-mail: jfernandezt@udc.es >> ---------------------------------------------------------------- >> >> >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]
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Dear Djie, Yes, the column headers have a name prepended to them. I think the problem is that there are two BEAD_STDERR (A and B) for each sample but Im not sure. I've also tried with lumiMethyR but I got another error... Enviado desde mi iPhone El 09/05/2012, a las 14:11, Djie Tjwan Thung <djie.thung@gmail.com> escribió: > Hi Juan, > > I'm not sure about this error, but I think it indicates that the header columns are in the wrong format. > > AVG_Beta, Avg_NBEADS_A, Avg_NBEADS_B, BEAD_STDERR_A, BEAD_STDERR_B, Signal_A, Signal_B, Detection.Pval, Intensity. > > Are you sure each of the above column names have a sample name prepended to them? I.e. sample1.AVG_Beta, sample1.Avg_NBEADS_A. > After the sample name there should be a dot that seperates the sample name and column name like AVG_Beta. > > If your file has a format like this, then I don't know the solution and you're better off waiting for someone to reply with more knowledge than me ;). > > Good luck, > > Djie > > > 2012/5/9 Juan Fernández Tajes <jfernandezt@udc.es> > Hi Djie: > > I´ve tried but I got another error..... > > Error in grep(dattypes$original[i], cn) : invalid 'pattern' argument > > Any more ideas? > > Thanks a lot > > > Juan > > --------------------------------------------------------------- > Juan Fernandez Tajes, ph. D > Grupo XENOMAR > Departamento de Biología Celular y Molecular > Facultad de Ciencias-Universidade da Coruña > Tlf. +34 981 167000 ext 2030 > e-mail: jfernandezt@udc.es > ---------------------------------------------------------------- > > > De: "Djie Tjwan Thung" <djie.thung@gmail.com> > Para: "Juan Fernández Tajes" <jfernandezt@udc.es> > CC: Bioconductor@r-project.org > Enviados: Miércoles, 9 de Mayo 2012 13:27:55 > Asunto: Re: [BioC] Human Illumina Methylation27k question > > > Hi Juan, > > Try the lumiMethyR function for reading in your final report instead of using the lumiR function. > > I.e.: > library(lumi) > fileName <- 'MET0007_1Ronda_2Ronda_FinalReport.txt' > x.lumi <- lumiMethyR(fileName) > > Good luck! > > Djie > > > 2012/5/9 Juan Fernández Tajes <jfernandezt@udc.es> > Dear list, > > It is possible to import GenomeStudio v1 data into R with lumi package? The headers in my GenomeStudio final report are these: > > AVG_Beta, Avg_NBEADS_A, Avg_NBEADS_B, BEAD_STDERR_A, BEAD_STDERR_B, Signal_A, Signal_B, Detection.Pval, Intensity. > > The code that I followed: > > library(lumi) > fileName <- 'MET0007_1Ronda_2Ronda_FinalReport.txt' > x.lumi <- lumiR.batch(fileName, columnNameGrepPattern=list(exprs='AVG_Beta', se.exprs='BEAD_STDERR', detection='Detection.Pval', beadNum='Avg_NBEADS'), inputAnnotation=F) > > The error that I got: > > Error en lumiR(file.i, parseColumnName = FALSE, convertNuID = FALSE, QC = FALSE, : > Different column numbers of exprs and se.exprs! Please check the input data format. > > my sessionInfo(): > > R version 2.14.0 (2011-10-31) > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > locale: > [1] es_ES.UTF-8/es_ES.UTF-8/es_ES.UTF-8/C/es_ES.UTF-8/es_ES.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] lumi_2.6.0 nleqslv_1.9.3 methylumi_2.0.13 Biobase_2.14.0 > > loaded via a namespace (and not attached): > [1] affy_1.32.1 affyio_1.22.0 annotate_1.32.3 AnnotationDbi_1.16.19 BiocInstaller_1.2.1 DBI_0.2-5 > [7] grid_2.14.0 hdrcde_2.15 IRanges_1.12.6 KernSmooth_2.23-7 lattice_0.20-6 MASS_7.3-18 > [13] Matrix_1.0-5 mgcv_1.7-14 nlme_3.1-103 preprocessCore_1.16.0 RSQLite_0.11.1 tools_2.14.0 > [19] xtable_1.7-0 zlibbioc_1.0.1 > > Any help would be very appreciated > > Juan > > --------------------------------------------------------------- > Juan Fernandez Tajes, ph. D > Grupo XENOMAR > Departamento de Biología Celular y Molecular > Facultad de Ciencias-Universidade da Coruña > Tlf. +34 981 167000 ext 2030 > e-mail: jfernandezt@udc.es > ---------------------------------------------------------------- > > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]
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Pan Du ▴ 440
@pan-du-4636
Last seen 10.2 years ago
Hi Juan The lumiMethyR function basically calls "methylumiR" function in methylumi package. I believe the column names in your file do not match the predefined format in the function. If possible, you can send me the top 200 rows of your file or just send me zipped data file if it is not too big. I can help you have a check. An alternative way to input methylation data is using "methylumIDAT" function to directly input the iDAT file. In this way you can avoid the header format issues. Check the help of "methylumIDAT" function for more details. Pan > Date: Wed, 9 May 2012 13:33:17 +0200 (CEST) > From: Juan Fern?ndez Tajes <jfernandezt at="" udc.es=""> > To: Djie Tjwan Thung <djie.thung at="" gmail.com=""> > Cc: Bioconductor at r-project.org > Subject: Re: [BioC] Human Illumina Methylation27k question > Message-ID: > ? ? ? ?<736487667.320495.1336563197758.JavaMail.root at ms1a.correo.udc.es> > Content-Type: text/plain > > Hi Djie: > > I??ve tried but I got another error..... > > Error in grep(dattypes$original[i], cn) : invalid 'pattern' argument > > Any more ideas? > > Thanks a lot > > Juan > > --------------------------------------------------------------- > Juan Fernandez Tajes, ph. D > Grupo XENOMAR > Departamento de Biolog??a Celular y Molecular > Facultad de Ciencias-Universidade da Coru??a > Tlf. +34 981 167000 ext 2030 > e-mail: jfernandezt at udc.es > ---------------------------------------------------------------- > > > > De: "Djie Tjwan Thung" <djie.thung at="" gmail.com=""> > Para: "Juan Fern??ndez Tajes" <jfernandezt at="" udc.es=""> > CC: Bioconductor at r-project.org > Enviados: Mi??rcoles, 9 de Mayo 2012 13:27:55 > Asunto: Re: [BioC] Human Illumina Methylation27k question > > Hi Juan, > > Try the lumiMethyR function for reading in your final report instead of using the lumiR function. > > I.e.: > library(lumi) > fileName <- 'MET0007_1Ronda_2Ronda_FinalReport.txt' > x.lumi <- lumiMethyR(fileName) > > Good luck! > > Djie > > > > 2012/5/9 Juan Fern??ndez Tajes < jfernandezt at udc.es > > > > Dear list, > > It is possible to import GenomeStudio v1 data into R with lumi package? The headers in my GenomeStudio final report are these: > > AVG_Beta, Avg_NBEADS_A, Avg_NBEADS_B, BEAD_STDERR_A, BEAD_STDERR_B, Signal_A, Signal_B, Detection.Pval, Intensity. > > The code that I followed: > > library(lumi) > fileName <- 'MET0007_1Ronda_2Ronda_FinalReport.txt' > x.lumi <- lumiR.batch(fileName, columnNameGrepPattern=list(exprs='AVG_Beta', se.exprs='BEAD_STDERR', detection='Detection.Pval', beadNum='Avg_NBEADS'), inputAnnotation=F) > > The error that I got: > > Error en lumiR(file.i, parseColumnName = FALSE, convertNuID = FALSE, QC = FALSE, : > Different column numbers of exprs and se.exprs! Please check the input data format. > > my sessionInfo(): > > R version 2.14.0 (2011-10-31) > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > locale: > [1] es_ES.UTF-8/es_ES.UTF-8/es_ES.UTF-8/C/es_ES.UTF-8/es_ES.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] lumi_2.6.0 nleqslv_1.9.3 methylumi_2.0.13 Biobase_2.14.0 > > loaded via a namespace (and not attached): > [1] affy_1.32.1 affyio_1.22.0 annotate_1.32.3 AnnotationDbi_1.16.19 BiocInstaller_1.2.1 DBI_0.2-5 > [7] grid_2.14.0 hdrcde_2.15 IRanges_1.12.6 KernSmooth_2.23-7 lattice_0.20-6 MASS_7.3-18 > [13] Matrix_1.0-5 mgcv_1.7-14 nlme_3.1-103 preprocessCore_1.16.0 RSQLite_0.11.1 tools_2.14.0 > [19] xtable_1.7-0 zlibbioc_1.0.1 > > Any help would be very appreciated > > Juan
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