Hi Jim The empirical evidence would suggest otherwise. :) Sigh. Perhaps I'll try submitting my question again sometime soon. Or perhaps biomaRt will become clearer if I use it more. Regards John --- -----Original Message----- From: James MacDonald [mailto:jmacdon@med.umich.edu] Sent: 23 January 2009 17:14 To: john seers (IFR) Subject: Re: [BioC] Help using biomaRt Hi John, If you expect any real help you will need to supply us with the code you have tried (especially a toy example that people can try themselves) and the exact output from R. Also, the output of sessionInfo(). Best, Jim

Looking back over this thread, it appears you got a lot of responses, for which you graciously thanked the responders. The only question I see that wasn't answered was at the end of an extremely long post in which you seemed to want to show your thinking when using biomaRt. I think this was the problem. Most people don't have the time to read all that, and probably don't care to know what worked for you. A short message showing what you tried and the unexpected result would suffice. As would reading the error message and trying to think what it might mean. You got Error in getBM(attnames, filters = filtnames, values = affyids, mart = mart) : Query ERROR: caught BioMart::Exception::Usage: Attributes from multiple attribute pages are not allowed after adding one new attribute. I don't know what this means, really, but it would appear that you can't mix ensembl_exon_id with the other attributes. > results3<-getBM("ensembl_exon_id", filters=filtnames, values=affyids, mart=mart) > results3 ensembl_exon_id 1 ENSMUSE00000614004 2 ENSMUSE00000704983 3 ENSMUSE00000641393 4 ENSMUSE00000617038 5 ENSMUSE00000617037 6 ENSMUSE00000617036 7 ENSMUSE00000560065 [snip] I understand your frustration with biomaRt. When I first started using it, I was frustrated as well. It's pretty complicated, but quite powerful as well. As with all software there is a learning curve, and there is no substitute for experience, and that only comes from trial and error. Best, Jim john seers (IFR) wrote: > > Hi Jim > > The empirical evidence would suggest otherwise. :) > > Sigh. Perhaps I'll try submitting my question again sometime soon. Or > perhaps biomaRt will become clearer if I use it more. > > Regards > > John > > > > > --- > > -----Original Message----- > From: James MacDonald [mailto:jmacdon at med.umich.edu] > Sent: 23 January 2009 17:14 > To: john seers (IFR) > Subject: Re: [BioC] Help using biomaRt > > Hi John, > > If you expect any real help you will need to supply us with the code you > have tried (especially a toy example that people can try themselves) and > the exact output from R. Also, the output of sessionInfo(). > > Best, > > Jim > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-5646 734-936-8662