Dear list,
I have a problem when I try to use the IlluminaHumanMethylation27k.db 
(in marticular the method IlluminaHumanMethylation27kCHR) package from a 
package I am writing.

In a previous post I asked how to integrate the information about the 
chromosomes in a MethyLumiM object. Tim (thanks for your help) suggested 
me this solution:

/fData(AML)$chrom<- as.factor(unlist(mget(featureNames(AML), 
IlluminaHumanMethylation27kCHR)))/

It works perfectly if I use it from command line. But when I launch the 
same command from my package I have the following error:

*/Error in mget(featureNames(lumiMethy), IlluminaHumanMethylation27kCHR) :
   second argument must be an environment/*
/
/Inside the namespace of my package, I import the entire package 
IlluminaHumanMethylation27k.db.
To solve the problem, I have already tried to use "as.environment()" and 
to require() the IlluminaHumanMethylation27k.db package inside mine. I 
tried also to use the function "getAnnMap" specifying as type "env". 
Nothing worked.

Any new suggestion is welcomed!!!

Many thanks!
Francesco


 > sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
  [1] tcltk     grid      splines   stats     graphics  grDevices 
utils     datasets  methods   base

other attached packages:
  [1] IlluminaHumanMethylation27k.db_1.4.0 
org.Hs.eg.db_2.4.6                   AnnotationDbi_1.12.0
  [4] HumMeth27QCReport_1.2.0              
RSQLite_0.9-4                        DBI_0.2-5
  [7] WriteXLS_2.1.0                       
plotrix_3.0-9                        gplots_2.8.0
[10] caTools_1.11                         
bitops_1.0-4.1                       gdata_2.8.1
[13] gtools_2.6.2                         
Hmisc_3.8-3                          survival_2.36-5
[16] amap_0.8-5                           
lumi_2.2.1                           methylumi_1.6.1
[19] Biobase_2.10.0

loaded via a namespace (and not attached):
  [1] affy_1.28.0           affyio_1.18.0         annotate_1.28.0       
cluster_1.13.3        hdrcde_2.15           KernSmooth_2.23-4
  [7] lattice_0.19-17       MASS_7.3-11           Matrix_0.999375-46    
mgcv_1.7-3            nlme_3.1-98           preprocessCore_1.12.0
[13] xtable_1.5-6



-- 

*Francesco Mattia Mancuso*
- Bioinformatician at Bioinformatics Core Facility
- Bioinformatician at Proteomics Core Facility

CRG-Centre for Genomic Regulation
C/ Dr. Aiguader, 88
Edif. PRBB
08003 Barcelona, Spain

Telephone: +34 933160202
francesco.mancuso@crg.es <mailto:francesco.mancuso@crg.es>
www.crg.es <http://pasteur.crg.es/portal/page/portal/Internet/>

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