[BioC] org.Sc.sgd.db: Yeast ensembl ID to entrez ID conversion problem

[Zhu, Julie]

Hi,

I have used org.Hs.egENSEMBL2EG in org.Hs.eg.db for mapping emsembl gene ID
to entrez ID successfully. However it does not work for org.Sc.sgd.db. I
tried to use org.Sc.sgdENSEMBL instead but got the ensembl ID back as
mapping. Here is the code snippet to show the problem and session info.

orgAnn <- get(paste("org.Sc.sgd", "ENSEMBL", sep = ""))
OrgAnn

IDs = c("YHR055C")
xx[names(xx)==IDs[1]]

###### output the ensembl id instead of entrez id #######
$YHR055C
[1] "YHR053C" "YHR055C"

# sessionInfo()
R version 2.10.0 (2009-10-26)
i386-apple-darwin8.11.1

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] org.Sc.sgd.db_2.3.5                 ChIPpeakAnno_1.3.15
limma_2.19.2       
 [4] org.Hs.eg.db_2.3.6                  GO.db_2.3.5
RSQLite_0.7-1      
 [7] DBI_0.2-4                           AnnotationDbi_1.8.1
BSgenome.Ecoli.NCBI.20080805_1.3.16
[10] BSgenome_1.14.2                     Biostrings_2.14.8
IRanges_1.4.9      
[13] multtest_2.1.2                      Biobase_2.5.5
biomaRt_2.1.0      

loaded via a namespace (and not attached):
[1] MASS_7.3-3      RCurl_0.98-1    splines_2.10.0  survival_2.35-7
tools_2.10.0    XML_2.3-0      ENSEMBL map for Yeast (object of class
"AnnDbBimap")



Thank you very much for your help!

Best regards,

Julie


*******************************************
Lihua Julie Zhu, Ph.D
Research Associate Professor
Program in Gene Function and Expression
University of Massachusetts Medical School
364 Plantation Street, Room 613
Worcester, MA 01605
508-856-5256
http://www.umassmed.edu/pgfe/faculty/zhu.cfm