Hello, I wonder if anyone has come across the same problem as I am having. I am trying to map a gene name i.e HGNC symbol to its corresponding affymetrix probe using R/Bioconductor but I don't seem to be able to do it using biomaRt I tried : getBM(attributes=c("affy_hg_u133_plus_2","hgnc_symbol","chromosome_nam e","band"),filters="affy_hg_u133_plus_2",values="CD86", mart=mart) and other similar code but they don't work The previous version of biomaRt that uses getFeature() worked when I use something like this : feat = getFeature(symbol = "CD86", type = "affy_hg_u133_plus_2", mart = mart) but I just can't seem to get the same to work using getBM which now superceeds getFeature has anyone come across the same problem and if so how did they solve it. Many thanks. Raphael. _________________________________________________________________ Get a bird?s eye view of the world with Multimap

is there some reason to not just use the mappings provided? > library(hgu133plus2.db) Loading required package: AnnotationDbi Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. r1Loading required package: DBI > r1 = revmap(hgu133plus2SYMBOL) > r1$"CD86" [1] "205685_at" "205686_s_at" "210895_s_at" > biomaRt is great, but why haul things across the internet you have on the local file system? best wishes Robert Ruppert Valentino wrote: > > Hello, > > I wonder if anyone has come across the same problem as I am having. > > I am trying to map a gene name i.e HGNC symbol to its corresponding affymetrix probe using R/Bioconductor but I don't seem to be able to do it using biomaRt > > I tried : > > getBM(attributes=c("affy_hg_u133_plus_2","hgnc_symbol","chromosome_n ame","band"),filters="affy_hg_u133_plus_2",values="CD86", mart=mart) > > and other similar code but they don't work > > The previous version of biomaRt that uses getFeature() worked when I use something like this : > > feat = getFeature(symbol = "CD86", type = "affy_hg_u133_plus_2", mart = mart) > > but I just can't seem to get the same to work using getBM which now superceeds getFeature > > has anyone come across the same problem and if so how did they solve it. > > Many thanks. > > Raphael. > > > _________________________________________________________________ > Get a bird?s eye view of the world with Multimap > > _______________________________________________ > 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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

Raphael. What if you 'filter' on the 'value' you are looking for, such as: > getBM (attributes =c("affy_hg_u133_plus_2","hgnc_symbol","chromosome_name","band"), filters="hgnc_symbol",values="CD86", mart=mart) affy_hg_u133_plus_2 hgnc_symbol chromosome_name band 1 205685_at CD86 3 q13.33 2 210895_s_at CD86 3 q13.33 3 205686_s_at CD86 3 q13.33 Cheers, Mark > sessionInfo() R version 2.8.0 (2008-10-20) i386-apple-darwin8.11.1 locale: en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_1.16.0 loaded via a namespace (and not attached): [1] RCurl_0.91-0 XML_1.98-1 On 08/12/2008, at 8:37 AM, Ruppert Valentino wrote: > > > Hello, > > I wonder if anyone has come across the same problem as I am having. > > I am trying to map a gene name i.e HGNC symbol to its corresponding > affymetrix probe using R/Bioconductor but I don't seem to be able to > do it using biomaRt > > I tried : > > getBM > (attributes > = > c > ("affy_hg_u133_plus_2 > ","hgnc_symbol > ","chromosome_name > ","band"),filters="affy_hg_u133_plus_2",values="CD86", mart=mart) > > and other similar code but they don't work > > The previous version of biomaRt that uses getFeature() worked when I > use something like this : > > feat = getFeature(symbol = "CD86", type = "affy_hg_u133_plus_2", > mart = mart) > > but I just can't seem to get the same to work using getBM which now > superceeds getFeature > > has anyone come across the same problem and if so how did they solve > it. > > Many thanks. > > Raphael. > > > _________________________________________________________________ > Get a bird?s eye view of the world with Multimap > > _______________________________________________ > 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 ------------------------------ Mark Robinson Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robinson at garvan.org.au e: mrobinson at wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852