[BioC] Help me understand org.Hs.eg.db

Daren Tan darentan76 at gmail.com
Sat Apr 4 06:06:55 CEST 2009

I am using two approaches to get EntrezID to genes mapping, as well as
genes to EntrezID mappings. toTable gives same number of mappings in
both directions, but mget doesn't. Which approach should I trust and
why ?

> dim(toTable(org.Hs.egSYMBOL2EG))
[1] 39824     2
> dim(toTable(org.Hs.egSYMBOL))
[1] 39824     2

> length(mget(mappedRkeys(org.Hs.egSYMBOL2EG), org.Hs.egSYMBOL2EG))
[1] 39800
> length(mget(mappedLkeys(org.Hs.egSYMBOL), org.Hs.egSYMBOL))
[1] 39824

> sessionInfo()
R version 2.8.1 (2008-12-22)

LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

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

other attached packages:
 [1] KEGG.db_2.2.5       GOstats_2.8.0       Category_2.8.4
genefilter_1.22.0   survival_2.34-1     RBGL_1.18.0
 [8] xtable_1.5-4        GO.db_2.2.5         graph_1.20.0
org.Hs.eg.db_2.2.6  RSQLite_0.7-1       DBI_0.2-4
[15] Biobase_2.2.2

loaded via a namespace (and not attached):
[1] cluster_1.11.12       gdata_2.4.2           gplots_2.6.0
GSEABase_1.4.0        gtools_2.5.0-1        xlsReadWritePro_1.4.0
[7] XML_2.1-0

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