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]]