On Wed, Oct 20, 2010 at 8:33 AM, Paolo Sonego <paolo.sonego@gmail.com>wrote:

> 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
>

Hi, Paolo.  You have some mismatches between the version of Bioconductor and
the packages listed here.  You will need to upgrade at least
the IlluminaHumanMethylation27k.db to version 1.4.0, the version for Bioc
2.7 and R 2.12.

Sean


> [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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

