Hi,

I have used org.Hs.egGO for mapping entrez ID in human to GO term successfully. However the mapping is not available in org.Sc.sgGO. So I tried to convert gene name to orf using org.Sc.sgdCOMMON2ORF mapping. Then I encountered the following error.

gene2orf = org.Sc.sgdCOMMON2ORF
mapped_gene <- mappedkeys(gene2orf)
xx <- as.list(gene2orf[mapped_genes])
Error in .checkKeys(value, Lkeys(x), x@ifnotfound) :
  value for "15S_rRNA" not found
Error in as.list(gene2orf[mapped_genes]) :
  error in evaluating the argument 'x' in selecting a method for function 'as.list

The session information is the same as the following post.

Thank you so much for your help!

Best regards,

Julie


On 3/23/10 9:43 AM, "Zhu, Julie" <Julie.Zhu@umassmed.edu> wrote:

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

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