[BioC] lumi: Methylation450 Data Input

Wong, Chao-Jen cwon2 at fhcrc.org
Thu Nov 3 19:07:25 CET 2011

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.  


----- Original Message -----
From: "Jiayi Sun" <monikasun88 at gmail.com>
To: bioconductor at r-project.org
Sent: Wednesday, November 2, 2011 12:32:16 PM
Subject: [BioC] lumi: Methylation450 Data Input


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)

 [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

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

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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 
cwon2 at fhcrc.org

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