Dear John, Thank you for reporting this. It looks like Ensembl migrated to a new version overnight and changed the attribute hgnc_symbol to hgnc without informing us. getGene has hgnc_symbol hardcoded in it and thus won't work. I would recommend to do your query using the more general getBM function. Meanwhile I'll update the getGene function asap. As you suggested, you can do the query via getBM and this is the recommended way as it works with all versions of Ensembl, here's how: getBM(c("affy_hg_u95av2","hgnc","ensembl_gene_id","chromosome_name","s tart_position","end_position","strand","description"), filters="affy_hg_u95av2", values="1939_at", mart=mart) Cheers, Steffen ----- Original Message ----- From: John Lande <john.lande77@gmail.com> Date: Thursday, October 25, 2007 4:00 am Subject: Re: [BioC] getGene type not recognized To: bioconductor at stat.math.ethz.ch > maybe I found the problems, but I will not be able to solve the issue: > > if I run the getBM command, everything works but if in the > attributes i put > the field hgnc_symbol, it complains with the same error: > > Error in getBM(attributes = c("affy_hg_u95av2", "hgnc_symbol", > "chromosome_name", : > Invalid attribute(s): hgnc_symbol > Please use the function 'listAttributes' to get valid attribute names > > if I run 'listAttributes' there is no hgnc_symbol, but hgnc. it is > possiblethat by default getGene still have this parameter ad default. > > > On 10/25/07, John Lande <john.lande77 at="" gmail.com=""> wrote: > > > > Dear BioC, > > > > > > I have the following problem with biomaRt packages: > > > > if I run any script with the function getGene, it seems it cannot > > recognize the type field. > > > > it happen also with the example in the man of getGene: > > > > >mart = useMart("ensembl", dataset="hsapiens_gene_ensembl") > > >g = getGene( id = "1939_at", type = "affy_hg_u95av2", mart = mart) > > >show(g) > > Error in getBM(attributes = attrib, filters = type, values = id, > mart = > > mart) : > > Invalid attribute(s): hgnc_symbol > > Please use the function 'listAttributes' to get valid attribute > names> > > in general I am having problems with this packages in these day, > when I am > > using long input. I handled this using shorter input, and then > merging the > > results, but now I dont know what to do. > > > > by the way I am running ubuntu 7.04. > > > > did someone have the notice the same? > > > > > > > > > sessionInfo() > > R version 2.6.0 (2007-10-03) > > x86_64-unknown-linux-gnu > > > > locale: > > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF- > 8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF- > 8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF- > 8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;L C_IDENTIFICATION=C > > > > > > attached base packages: > > [1] tools stats graphics grDevices utils datasets > methods> [8] base > > > > other attached packages: > > [1] Biobase_1.17.0 biomaRt_1.12.0 RCurl_0.8-3 > > [4] mouseLLMappings_2.0.1 > > > > loaded via a namespace (and not attached): > > [1] rcompgen_0.1-17 XML_1.93-2 > > > > > > > > thank you > > > > [[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

Hi John, You did find the problem. Ensembl has a very bad habit of changing the names they use for things, which makes maintaining biomaRt difficult for Steffen (and by extension, maintaining affycoretools for me). <rant> This is an example of what I would consider a gratuitous change - was it really necessary to change hgnc_symbol to hgnc? Did we gain something here? They did something similar with Mus musculus and Rattus norvegicus as well, changing it to markersymbol. Again, did we _really_ gain something by making these changes? Can't we just call it a symbol for all species and go on with our lives? >:# </rant> Whew, I feel better now ;-D Best, Jim John Lande wrote: > maybe I found the problems, but I will not be able to solve the issue: > > if I run the getBM command, everything works but if in the attributes i put > the field hgnc_symbol, it complains with the same error: > > Error in getBM(attributes = c("affy_hg_u95av2", "hgnc_symbol", > "chromosome_name", : > Invalid attribute(s): hgnc_symbol > Please use the function 'listAttributes' to get valid attribute names > > if I run 'listAttributes' there is no hgnc_symbol, but hgnc. it is possible > that by default getGene still have this parameter ad default. > > > On 10/25/07, John Lande <john.lande77 at="" gmail.com=""> wrote: >> Dear BioC, >> >> >> I have the following problem with biomaRt packages: >> >> if I run any script with the function getGene, it seems it cannot >> recognize the type field. >> >> it happen also with the example in the man of getGene: >> >>> mart = useMart("ensembl", dataset="hsapiens_gene_ensembl") >>> g = getGene( id = "1939_at", type = "affy_hg_u95av2", mart = mart) >>> show(g) >> Error in getBM(attributes = attrib, filters = type, values = id, mart = >> mart) : >> Invalid attribute(s): hgnc_symbol >> Please use the function 'listAttributes' to get valid attribute names >> >> in general I am having problems with this packages in these day, when I am >> using long input. I handled this using shorter input, and then merging the >> results, but now I dont know what to do. >> >> by the way I am running ubuntu 7.04. >> >> did someone have the notice the same? >> >> >> >>> sessionInfo() >> R version 2.6.0 (2007-10-03) >> x86_64-unknown-linux-gnu >> >> locale: >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en _US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_ US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UT F-8;LC_IDENTIFICATION=C >> >> >> attached base packages: >> [1] tools stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] Biobase_1.17.0 biomaRt_1.12.0 RCurl_0.8-3 >> [4] mouseLLMappings_2.0.1 >> >> loaded via a namespace (and not attached): >> [1] rcompgen_0.1-17 XML_1.93-2 >> >> >> >> thank you >> > > [[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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623