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
>
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>
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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
> 206.667.4485
> cwon2@fhcrc.org
>
>
>


-- 
Jiayi Monika Sun
Rice University, Bioengineering '10
Baylor College of Medicine Graduate School, SCBMB
jmsun@bcm.edu

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