[BioC] Inconsistency in illuminaHumanv4.db ?

Holger [guest] guest at bioconductor.org
Wed Nov 30 01:39:40 CET 2011

I am using illuminaHumanv4.db for my research, so first of all,  thank you for maintaining this very valuable package!

When working with the illuminaHumanv4listNewMappings, I realised that some genomic coordinates are separated with " " instead of ",". Almost all other multiple entries are separated with a ",". Additionlly, genomic position of those entries does not seem to match with ucsc hg19 browser:

test <- illuminaHumanv4fullReannotation()
grep(" ", test$GenomicLocation, value=T)
[1] "chr9:70645819:70645844:+ chr9:68298969:68298994:+ chr9:42251008:42251033:+ chr9:45442520:45442545:+"
[2] "chr19:53832784:53832812:+ chr19:53268654:53268682:+"                                                
[3] "chr7:142008849:142008868:+ chr1:161139601:161139616:+"                                              
[4] "chr7:142008849:142008868:+ chr1:161139601:161139616:+"                                              
[5] "chrX:71034915:71034941:+ chrX:70888863:70888889:+ chrX:70885403:70885429:+"                         
[6] "chrX:71034915:71034941:+ chrX:70888863:70888889:+ chrX:70885403:70885429:+"                         
[7] "chr22:18979472:18979497:+ chrX:70888863:70888889:+ chrX:70885403:70885429:+"                        
[8] "chr1:149906516:149906531:+ chr1:185572746:185572761:+"                                              
[9] "chr1:176811981:176811996:+ chr1:161139601:161139616:+"        

Is there any specific reason for this?

When looking on illuminaHumanv4.db_1.10.0, other probes were effected, but the problem appeared to be present, too.

 -- output of sessionInfo(): 

R version 2.14.0 (2011-10-31)
Platform: i386-pc-mingw32/i386 (32-bit)

[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252   
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C                   
[5] LC_TIME=German_Germany.1252    

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

other attached packages:
[1] illuminaHumanv4.db_1.12.1 org.Hs.eg.db_2.6.4       
[3] RSQLite_0.10.0            DBI_0.2-5                
[5] AnnotationDbi_1.16.5      Biobase_2.14.0           

loaded via a namespace (and not attached):
[1] IRanges_1.12.3

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