Hi, Sorry for the long email, I have two questions towards using GOstats for illumina mouse-6 data: 1-- I couldn't find the annotation package for illumina mouse-6 arrays under the downloads link, Is there a way for me to generate it myself? I do have the annotation information for the platform? 2--I tried to generated the entrez list for all the genes from the chip through the following code -- ulist is list of gene symbol from the chip x <- org.Mm.egSYMBOL2EG mapped_genes <- mappedkeys(x) xx <- as.list(x[mapped_genes]) ulist.entrez<-xx[ulist] ulist.e <- unlist(glist.entrez,use.names=F) The problem of my code is there was original 20183 symbols, after remove the duplications(multiple probes for one gene), I got 14430 genes. But only 244 of them have entrez ids -- which makes no GO term significant. > glist.entrez[1:5] $`1110012J17Rik` [1] "68617" $<na> NULL $`1110032E23Rik` [1] "68659" $<na> NULL $<na> NULL I am not sure what I did wrong? or how to get around this problem? Thanks, Yupu

Hi Yupu, To learn how to make a custom package, please see the SQLForge vignette in the AnnotationDbi package. You can find it here: http://www.bioconductor.org/packages/devel/bioc/html/AnnotationDbi.htm l Marc Yupu Liang wrote: > Hi, > > Sorry for the long email, > > I have two questions towards using GOstats for illumina mouse-6 data: > > 1-- I couldn't find the annotation package for illumina mouse-6 arrays > under the downloads link, > > Is there a way for me to generate it myself? I do have the annotation > information for the platform? > > 2--I tried to generated the entrez list for all the genes from the > chip through the following code -- ulist is list of gene symbol from > the chip > > x <- org.Mm.egSYMBOL2EG > mapped_genes <- mappedkeys(x) > xx <- as.list(x[mapped_genes]) > > ulist.entrez<-xx[ulist] > ulist.e <- unlist(glist.entrez,use.names=F) > > The problem of my code is there was original 20183 symbols, after > remove the duplications(multiple probes for one gene), I got 14430 genes. > But only 244 of them have entrez ids -- which makes no GO term > significant. > > > glist.entrez[1:5] > > $`1110012J17Rik` > [1] "68617" > > $<na> > NULL > > $`1110032E23Rik` > [1] "68659" > > $<na> > NULL > > $<na> > NULL > > > I am not sure what I did wrong? or how to get around this problem? > > Thanks, > Yupu > > _______________________________________________ > 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 >

Hi, The annotation you need should already be in Bioconductor. If you are trying to analyze the output of BeadStudio, you can run one of the following in R depending on what the platform is:- biocLite("illuminaMousev1.db") biocLite("illuminaMousev1p1.db") biocLite("illuminaMousev2.db") or with the bead-level data, one of the following biocLite("illuminaMousev1BeadID.db") biocLite("illuminaMousev1p1BeadID.db") biocLite("illuminaMousev2BeadID.db") Hope this helps, Mark On Fri, Oct 2, 2009 at 12:56 AM, Yupu Liang <liang at="" cbio.mskcc.org=""> wrote: > Hi, > > Sorry for the long email, > > I have two questions towards using GOstats for illumina mouse-6 data: > > 1-- I couldn't find the annotation package for illumina mouse-6 arrays under > the downloads link, > > Is there a way for me to generate it myself? I do have the annotation > information for the platform? > > 2--I tried to generated the entrez list for all the genes from the chip > through the following code -- ulist is list of gene symbol from the chip > > x <- org.Mm.egSYMBOL2EG > mapped_genes <- mappedkeys(x) > xx <- as.list(x[mapped_genes]) > > ulist.entrez<-xx[ulist] > ulist.e <- unlist(glist.entrez,use.names=F) > > The problem of my code is there was original 20183 symbols, after remove the > duplications(multiple probes for one gene), I got 14430 genes. > But only 244 of them have entrez ids -- which makes no GO term significant. > >> glist.entrez[1:5] > > $`1110012J17Rik` > [1] "68617" > > $<na> > NULL > > $`1110032E23Rik` > [1] "68659" > > $<na> > NULL > > $<na> > NULL > > > I am not sure what I did wrong? or how to get around this problem? > > Thanks, > Yupu > > _______________________________________________ > 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 >