Thanks Fred and Martin. ---- On Sun, 06 May 2012 08:28:58 -0700 Martin Morgan <mtmorgan@fhcrc.org> wrote ---- On 05/06/2012 07:23 AM, Fred Boehm wrote: > Greetings, Michelle, > > I haven't worked with mouse data, but I think that the function getBM() > in the bioconductor package biomaRt can help. also library(mouse4302.db) unlist(mget(fit$genes$ID, mouse4302ENSEMBL, ifnotfound=NA) or even better in R 2.14.0 or greater select(mouse4302.db, ids, "ENSEMBL") (see ?select, ?keys, ?cols, ?keytype) Martin > > For instance, one could use the code below (replacing mySymbols with the > vector of symbols that interest you) to output a data.frame with both > ensembl gene ID and mgi symbol. > > The creators of biomaRt have generated some nice tutorial materials and > posted them at: > > http://www.bioconductor.org/packages/2.2/bioc/html/biomaRt.html > > If I've misinterpreted your question, you may be able to find the answer > by viewing the biomaRt materials. > > I hope that this helps. > > Cheers, > Fred > -------------- > > source("http://bioconductor.org/biocLite.R") > biocLite("biomaRt") > > library(biomaRt) > mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl") > listFilters(mouse) > listAttributes(mouse) > mySymbols<- "2310015A10Rik" # mySymbols is a vector of MGI symbols. > getBM( attributes=c("ensembl_gene_id", "mgi_symbol") , filters= > "mgi_symbol" , values =mySymbols ,mart=mouse) > > > > > On 5/6/12 5:41 AM, michelle_low wrote: >> Hi all, >> >> I have a list of gene symbols generated from the differential expression analysis below. How do I convert these symbols to emsembl id? Thanks >> >> >> Regards, >> Michelle >> >> >> >> >> R version 2.14.1 (2011-12-22) >> Platform: x86_64-pc-mingw32/x64 (64-bit) >> >> >> > library(affy) >> > library(limma) >> > pd=read.AnnotatedDataFrame("phenodata.txt",header=TR UE,sep="",row.names=1) >> > a=ReadAffy(filenames=rownames(pData(pd)),phenoData=pd,verbose=TRUE) >> 1 reading Control-1.cel ...instantiating an AffyBatch (intensity a 1004004x6 matrix)...done. >> Reading in : Control-1.cel >> Reading in : Control-2.cel >> Reading in : Dicer-1.cel >> Reading in : Dicer-2.cel >> Reading in : Drosha-1.cel >> Reading in : Drosha-2.cel >> > x=rma(a) >> Loading required package: AnnotationDbi >> Background correcting >> Normalizing >> Calculating Expression >> Warning message: >> package âEUR~AnnotationDbiâEUR^(TM) was built under R version 2.14.2 >> > c=paste(pd$treatment,pd$n,sep="") >> > f=factor(c) >> > design=model.matrix(~0+f) >> > colnames(design)=levels(f) >> > fit=lmFit(x,design) >> > library(mouse4302.db) >> Loading required package: org.Mm.eg.db >> Loading required package: DBI >> >> Warning messages: >> 1: package âEUR~RSQLiteâEUR^(TM) was built under R version 2.14.2 >> 2: package âEUR~DBIâEUR^(TM) was built under R version 2.14.2 >> > library(annotate) >> Warning message: >> package âEUR~annotateâEUR^(TM) was built under R version 2.14.2 >> > fit$genes$Symbol<- getSYMBOL(fit$genes$ID,"mouse4302.db") >> > contrast.matrix=makeContrasts(E1="present- absent.Dicer",E2="present-absent.Drosha",E3="absent.Drosha- absent.Dicer",levels=design) >> > fit2=contrasts.fit(fit,contrast.matrix) >> > >> > fit2=eBayes(fit2) >> > >> > results1<-topTable (fit2, coef=1, p.value=0.0001,number=nrow(fit2)) >> > write.table(results1, file="control-Dicer5.txt") >> > results2<-topTable (fit2, coef=2, p.value=0.0001,number=nrow(fit2)) >> > write.table(results2, file="control-Drosha5.txt") >> > results3<-topTable (fit2, coef=3, p.value=0.0001,number=nrow(fit2)) >> > results=decideTests(fit2) >> > summary(results2) >> > b=venncounts(results2) >> > print(b) >> > vennDiagram(results) >> > a=vennDiagram(results,include=c("up","down"),counts. col=c("red","green")) >> >> >> >> [[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 > > [[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 -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793 [[alternative HTML version deleted]]