[BioC] Processing of Illumina Infinium methylation microarray data using lumi - addColorChannelInfo bug?
Paolo Sonego
paolo.sonego at gmail.com
Wed Oct 20 14:33:00 CEST 2010
Hi guys,
I'm trying to analyze some Illumina Infinium methylation microarray data
using the new lumi package (btw, great improvement and nice brand new
methylation vignette).
The following error is produced when trying to replicate the example in
the addColorChannelInfo() manual
> ?addColorChannelInfo
> data(example.lumiMethy)
> head(pData(featureData(example.lumiMethy)))
CHR COLOR_CHANNEL
cg00002426 3 Red
cg00012386 1 Red
cg00013618 22 Grn
cg00014837 12 Red
cg00020533 6 Red
cg00021527 17 Red
> # removing color channel information
> testData = example.lumiMethy
> pData(featureData(testData))$COLOR_CHANNEL = NULL
> testData = addColorChannelInfo(testData,
lib="IlluminaHumanMethylation27k.db")
Loading required package: IlluminaHumanMethylation27k.db
Loading required package: AnnotationDbi
Loading required package: org.Hs.eg.db
Loading required package: DBI
Error in get(paste(sub("\\.db$", "", lib), "COLORCHANNEL", sep = "")) :
object 'IlluminaHumanMethylation27kCOLORCHANNEL' not found
> # check whether the color channel information is added
> head(pData(featureData(testData)))
CHR
cg00002426 3
cg00012386 1
cg00013618 22
cg00014837 12
cg00020533 6
cg00021527 17
Is this a bug?
Any help would be appreciated!
Thanks!
Paolo
Here is the output of my sessionInfo():
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] IlluminaHumanMethylation27k.db_1.2.0 org.Hs.eg.db_2.4.5
[3] RSQLite_0.9-2 DBI_0.2-5
[5] AnnotationDbi_1.12.0 lumi_2.2.0
[7] Biobase_2.10.0 fortunes_1.4-0
loaded via a namespace (and not attached):
[1] affy_1.28.0 affyio_1.18.0 annotate_1.28.0
[4] grid_2.12.0 hdrcde_2.14 KernSmooth_2.23-4
[7] lattice_0.19-13 MASS_7.3-8 Matrix_0.999375-44
[10] methylumi_1.4.0 mgcv_1.6-2 nlme_3.1-97
[13] preprocessCore_1.12.0 tools_2.12.0 xtable_1.5-6
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