Nope, you are correct. I have been working too long today…

On Nov 26, 2012, at 8:41 PM, Steve Lianoglou <mailinglist.honeypot@gmail.com> wrote:

> Hi,
> 
> I'm not sure, but did you just realize that you used two different entrez id's for your test, eg:
> 
> revmap(org.Hs.egENSEMBL2EG)[['1019']]
> org.Hs.egENSEMBL[['11019']]
> 
> Or do you think you are seeing a different problem?
> 
> Not sure where you think "the truncating" is happening
> 
> 
> 
> On Monday, November 26, 2012, John St. John wrote:
> Foot-in-mouth, found the bug, my typo, I truncated a 1 in my test.
> 
> http://www.ncbi.nlm.nih.gov/gene?term=11019
> 
> Looks like *maybe* the entrez ids are getting truncated in some of these databases or something, which could cause this problem.
> 
> 
> Looks like the output is the same
> 
> On Nov 26, 2012, at 8:18 PM, John St. John <johnthesaintjohn@gmail.com> wrote:
> 
> > I have a gene for example, CDK4 http://www.ncbi.nlm.nih.gov/gene?term=1019, and I was testing its mapping between entrez ID and ENSEMBL id in R. It's entrez id is 1019.
> >
> > library(org.Hs.eg.db)
> >
> > revmap(org.Hs.egENSEMBL2EG)[['1019']]
> > [1] "ENSG00000135446"
> >
> > #this appears to be the expected output (see http://www.ncbi.nlm.nih.gov/gene?term=1019)
> >
> > org.Hs.egENSEMBL[['11019']]
> > [1] "ENSG00000121897"
> >
> > #wrong output, this is a different unrelated gene, LIAS
> >
> > org.Hs.egSYMBOL[['11019']]
> > [1] "LIAS"
> >
> > #expected "CDK4"
> >
> > Help description for org.Hs.egENSEMBL:
> > org.Hs.egENSEMBL is an R object that contains mappings between Entrez Gene identifiers and Ensembl gene accession numbers.
> >
> > Help description for org.Hs.egENSEMBL2EG (it is the same help message):
> > org.Hs.egENSEMBL is an R object that contains mappings between Entrez Gene identifiers and Ensembl gene accession numbers.
> >
> > Help description for org.Hs.egSYMBOL:
> > org.Hs.egSYMBOL is an R object that provides mappings between entrez gene identifiers and gene abbreviations.
> >
> > There is something wrong here, right? From the helps it looks like these different annotation databases do the mappings I expect, and should all work with entrez ids as input. The fact that one of these works, and the rest do not is concerning. Is there a more widely used, less buggy mapping between ENSEMBL and Entrez that I should be using instead of this one?
> >
> > Thanks,
> > John
> >
> 
> 
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> 
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> 
> -- 
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact


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