[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)))
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))$COLOR_CHANNEL = NULL
 >  testData = addColorChannelInfo(testData, 
Loading required package: IlluminaHumanMethylation27k.db
Loading required package: AnnotationDbi
Loading required package: org.Hs.eg.db
Loading required package: DBI
Error in get(paste(sub("\\.db$", "", lib), "COLORCHANNEL", sep = "")) :
   object 'IlluminaHumanMethylation27kCOLORCHANNEL' not found
 > # check whether the color channel information is added
 >  head(pData(featureData(testData)))
cg00002426   3
cg00012386   1
cg00013618  22
cg00014837  12
cg00020533   6
cg00021527  17

Is this a bug?
Any help would be appreciated!


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)

[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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