lumi: Methylation450 Data Input
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Jiayi Sun ▴ 40
@jiayi-sun-4938
Last seen 7.0 years ago
Hello, I am new to using the lumi program for methylation analysis of the Illumina HumanMethylation450 data. I have the FinalReport.txt output from GenomeStudio. Would this file be sufficient for creating the lumibatch file? I am getting a read warning which returns me: filename <- "FinalReport.txt" procfile <- lumiMethyR(filename, "IlluminaHumanMethylation450k.db") qcfile specification is not supported for Final Report type BeadStudio Export files > sessionInfo() R version 2.13.1 (2011-07-08) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] lumi_2.5.7 nleqslv_1.9.0 methylumi_1.8.0 Biobase_2.12.1 [5] ggplot2_0.8.9 proto_0.3-9.2 reshape_0.8.4 plyr_1.5.2 loaded via a namespace (and not attached): [1] affy_1.30.0 affyio_1.20.0 annotate_1.30.0 [4] AnnotationDbi_1.14.1 DBI_0.2-5 hdrcde_2.15 [7] KernSmooth_2.23-6 lattice_0.19-30 MASS_7.3-13 [10] Matrix_0.999375-50 mgcv_1.7-6 nlme_3.1-101 [13] preprocessCore_1.14.0 RSQLite_0.9-4 xtable_1.5-6 -- Jiayi Monika Sun Rice University, Bioengineering '10 Baylor College of Medicine Graduate School, SCBMB jmsun@bcm.edu [[alternative HTML version deleted]]
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Chao-Jen Wong ▴ 580
@chao-jen-wong-3603
Last seen 9.3 years ago
USA/Seattle/Fred Hutchinson Cancer Reseā€¦
Hi, Jiayi, Your "FinalReport.txt" (I guess it is the sample profile output containing methylation data and other annotation columns) is sufficient to create a MethyLumiM (not LumiBatch) class object. If you wish to perform QC control and preprocess the data, you will need to export the control probe profile from GenomeStudio and feed it into the MethyLumiM object by ## suppose "qcfile.txt" if the control probe profile generated from GenomeStudio profile <- lumiMethyR(filename="FinalReport.txt", qcfile="qcfile.txt", lib="IlluminaHumanMethylation450k.db") Note that if you are going to do color adjustment and normalization using the lumi package, you have to make sure that "FinalReport.txt" contains the "COLOR_CHANNEL" column, which is not a default output coloumn in GenomeStudio. Chao-Jen ----- Original Message ----- From: "Jiayi Sun" <monikasun88@gmail.com> To: bioconductor at r-project.org Sent: Wednesday, November 2, 2011 12:32:16 PM Subject: [BioC] lumi: Methylation450 Data Input Hello, I am new to using the lumi program for methylation analysis of the Illumina HumanMethylation450 data. I have the FinalReport.txt output from GenomeStudio. Would this file be sufficient for creating the lumibatch file? I am getting a read warning which returns me: filename <- "FinalReport.txt" procfile <- lumiMethyR(filename, "IlluminaHumanMethylation450k.db") qcfile specification is not supported for Final Report type BeadStudio Export files > sessionInfo() R version 2.13.1 (2011-07-08) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] lumi_2.5.7 nleqslv_1.9.0 methylumi_1.8.0 Biobase_2.12.1 [5] ggplot2_0.8.9 proto_0.3-9.2 reshape_0.8.4 plyr_1.5.2 loaded via a namespace (and not attached): [1] affy_1.30.0 affyio_1.20.0 annotate_1.30.0 [4] AnnotationDbi_1.14.1 DBI_0.2-5 hdrcde_2.15 [7] KernSmooth_2.23-6 lattice_0.19-30 MASS_7.3-13 [10] Matrix_0.999375-50 mgcv_1.7-6 nlme_3.1-101 [13] preprocessCore_1.14.0 RSQLite_0.9-4 xtable_1.5-6 -- Jiayi Monika Sun Rice University, Bioengineering '10 Baylor College of Medicine Graduate School, SCBMB jmsun at bcm.edu [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Chao-Jen Wong Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., M1-B514 PO Box 19024 Seattle, WA 98109 206.667.4485 cwon2 at fhcrc.org
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Thanks a lot for your help, I will try this! On Thu, Nov 3, 2011 at 1:07 PM, Wong, Chao-Jen <cwon2@fhcrc.org> wrote: > Hi, Jiayi, > > Your "FinalReport.txt" (I guess it is the sample profile output containing > methylation data and other annotation columns) is sufficient to create a > MethyLumiM (not LumiBatch) class object. If you wish to perform QC control > and preprocess the data, you will need to export the control probe profile > from GenomeStudio and feed it into the MethyLumiM object by > > ## suppose "qcfile.txt" if the control probe profile generated from > GenomeStudio > profile <- lumiMethyR(filename="FinalReport.txt", qcfile="qcfile.txt", > lib="IlluminaHumanMethylation450k.db") > > Note that if you are going to do color adjustment and normalization using > the lumi package, you have to make sure that "FinalReport.txt" contains the > "COLOR_CHANNEL" column, which is not a default output coloumn in > GenomeStudio. > > Chao-Jen > > ----- Original Message ----- > From: "Jiayi Sun" <monikasun88@gmail.com> > To: bioconductor@r-project.org > Sent: Wednesday, November 2, 2011 12:32:16 PM > Subject: [BioC] lumi: Methylation450 Data Input > > Hello, > > I am new to using the lumi program for methylation analysis of the Illumina > HumanMethylation450 data. > > I have the FinalReport.txt output from GenomeStudio. Would this file be > sufficient for creating the lumibatch file? I am getting a read warning > which returns me: > > filename <- "FinalReport.txt" > procfile <- lumiMethyR(filename, "IlluminaHumanMethylation450k.db") > qcfile specification is not supported for Final Report type BeadStudio > Export files > > > sessionInfo() > R version 2.13.1 (2011-07-08) > Platform: x86_64-redhat-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] lumi_2.5.7 nleqslv_1.9.0 methylumi_1.8.0 Biobase_2.12.1 > [5] ggplot2_0.8.9 proto_0.3-9.2 reshape_0.8.4 plyr_1.5.2 > > loaded via a namespace (and not attached): > [1] affy_1.30.0 affyio_1.20.0 annotate_1.30.0 > [4] AnnotationDbi_1.14.1 DBI_0.2-5 hdrcde_2.15 > [7] KernSmooth_2.23-6 lattice_0.19-30 MASS_7.3-13 > [10] Matrix_0.999375-50 mgcv_1.7-6 nlme_3.1-101 > [13] preprocessCore_1.14.0 RSQLite_0.9-4 xtable_1.5-6 > > -- > Jiayi Monika Sun > Rice University, Bioengineering '10 > Baylor College of Medicine Graduate School, SCBMB > jmsun@bcm.edu > > [[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 > > -- > Chao-Jen Wong > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Avenue N., M1-B514 > PO Box 19024 > Seattle, WA 98109 > 206.667.4485 > cwon2@fhcrc.org > > > -- Jiayi Monika Sun Rice University, Bioengineering '10 Baylor College of Medicine Graduate School, SCBMB jmsun@bcm.edu [[alternative HTML version deleted]]
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