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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