[BioC] problem with 'FDb.InfiniumMethylation.hg19'

[Victoria Svinti]

Hi there,

I came across another error when trying to load this annotation:

obj <- lumiMethyR(fileName, lib="FDb.InfiniumMethylation.hg19")
Error in get(paste(sub("\\.db$", "", lib), "COLORCHANNEL", sep = "")) : 
  object 'FDb.InfiniumMethylation.hg19COLORCHANNEL' not found

Does anyone else have this problem? Also, I still get the 'condition has length > 1 …' error after downloading BSgenome.Hsapiens.UCSC.hg19... 

Would appreciate your thoughts.

Thanks,
Vicky

----

> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] annotate_1.38.0                    BiocInstaller_1.10.2              
 [3] FDb.InfiniumMethylation.hg19_1.0.1 rtracklayer_1.20.2                
 [5] Biostrings_2.28.0                  GenomicFeatures_1.12.2            
 [7] AnnotationDbi_1.22.6               GenomicRanges_1.12.4              
 [9] IRanges_1.18.1                     methylumi_2.6.1                   
[11] ggplot2_0.9.3.1                    reshape2_1.2.2                    
[13] scales_0.2.3                       lumi_2.12.0                       
[15] Biobase_2.20.0                     BiocGenerics_0.6.0                

loaded via a namespace (and not attached):
 [1] affy_1.38.1                        affyio_1.28.0                     
 [3] beanplot_1.1                       biomaRt_2.16.0                    
 [5] bitops_1.0-5                       BSgenome_1.28.0                   
 [7] BSgenome.Hsapiens.UCSC.hg19_1.3.19 colorspace_1.2-2                  
 [9] DBI_0.2-7                          dichromat_2.0-0                   
[11] digest_0.6.3                       grid_3.0.0                        
[13] gtable_0.1.2                       illuminaio_0.2.0                  
[15] KernSmooth_2.23-10                 labeling_0.2                      
[17] lattice_0.20-15                    limma_3.16.5                      
[19] MASS_7.3-26                        Matrix_1.0-12                     
[21] matrixStats_0.8.1                  mclust_4.1                        
[23] mgcv_1.7-24                        minfi_1.6.0                       
[25] multtest_2.16.0                    munsell_0.4                       
[27] nleqslv_2.0                        nlme_3.1-109                      
[29] nor1mix_1.1-4                      plyr_1.8                          
[31] preprocessCore_1.22.0              proto_0.3-10                      
[33] RColorBrewer_1.0-5                 RCurl_1.95-4.1                    
[35] reshape_0.8.4                      R.methodsS3_1.4.2                 
[37] Rsamtools_1.12.3                   RSQLite_0.11.4                    
[39] siggenes_1.34.0                    splines_3.0.0                     
[41] stats4_3.0.0                       stringr_0.6.2                     
[43] survival_2.37-4                    tools_3.0.0                       
[45] XML_3.98-1.1                       xtable_1.7-1                      
[47] zlibbioc_1.6.0                    
> 

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