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 > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > 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 [[alternative HTML version deleted]]