Question: org.Sc.sgd.db: Yeast ensembl ID to entrez ID conversion problem
0
gravatar for Julie Zhu
9.1 years ago by
Julie Zhu4.0k
United States
Julie Zhu4.0k 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
go yeast • 1.3k views
ADD COMMENTlink modified 9.1 years ago • written 9.1 years ago by Julie Zhu4.0k
Answer: org.Sc.sgd.db: Yeast ensembl ID to entrez ID conversion problem
0
gravatar for Julie Zhu
9.1 years ago by
Julie Zhu4.0k
United States
Julie Zhu4.0k wrote:
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 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
ADD COMMENTlink written 9.1 years ago by Julie Zhu4.0k
Hi Julie, The thing to understand about the yeast package org.Sc.sgd.db, is that it is not Entrez Gene based. It is SGD based instead (which is why it has the strange looking name and also why the primary keys are not entrez gene IDs). It does have entrez gene ID mappings however which can be accessed using org.Sc.sgdENTREZID as well as GO mappings which can be accessed using org.Sc.sgdGO and it seems that you found the mapping for ensembl gene IDs. It's not completely clear to me from your posts what you were trying for. But here are some examples of using the ID you gave to get results back for GO, Entrez Gene ID and Ensembl: ID = "YHR055C" # get Entrez Gene ID get(ID, org.Sc.sgdENTREZID) # get ensembl Gene ID get(ID, org.Sc.sgdENSEMBL) # get GO terms get(ID, org.Sc.sgdGO) Hope this helps? Let me know if it doesn't and we can make it work. Marc On 03/23/2010 07:38 AM, Zhu, Julie wrote: > 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 at 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 at="" 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >
ADD REPLYlink written 9.1 years ago by Marc Carlson7.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 139 users visited in the last hour