Thanks Steffen for the helpful answers. "description", how embarrassing! On Thu, Sep 13, 2012 at 11:42 AM, Steffen Durinck <durinck.steffen at="" gene.com=""> wrote: > Hi Juliet, > > The third attribute you're looking for is 'description': > > idens <- getBM(attributes = c("affy_hg_u133a","hgnc_symbol","description"), > filters ="affy_hg_u133a",values = probeSets, mart = ensembl) > > Gives: > > affy_hg_u133a hgnc_symbol > description > 1 219666_at MS4A6A membrane-spanning 4-domains, > subfamily A, member 6A [Source:HGNC Symbol;Acc:13375] > 2 220547_s_at FAM35B family with sequence > similarity 35, member B [Source:HGNC Symbol;Acc:31425] > 3 218034_at FIS1 fission 1 (mitochondrial outer membrane) homolog > (S. cerevisiae) [Source:HGNC Symbol;Acc:21689] > 4 220547_s_at FAM35B2 family with sequence similarity 35, member > B2 (pseudogene) [Source:HGNC Symbol;Acc:34038] > 5 220547_s_at FAM35A family with sequence > similarity 35, member A [Source:HGNC Symbol;Acc:28773] > > > There is no systematic way to figure out with attribute name you need to use > all you have is the attribute name and a description of the attribute. The > more you get used to looking at those, the easier it gets to figure out > which one you need and once you know the attributes you need, often you'll > be using a similar set of attributes most of the time > > > It is interesting to see in your example that one probeset maps to three > different but closely related genes. In the past I thought Ensembl would > remove such unambiguous mappers. I think the best to do in this case is to > remove all probes that map to multiple genes as there is no way to tell > which gene you'll be measuring. I'll report this example to the Ensembll > team as they used to do this for us. > > Cheers, > Steffen > > On Thu, Sep 13, 2012 at 8:29 AM, Juliet Hannah <juliet.hannah at="" gmail.com=""> > wrote: >> >> All, >> >> I am trying to create the GSEA chip file. This example uses Affy data, >> and the chip file is already available. I'm >> doing this as an exercise in preparation for other platforms. >> >> The chip file should look like: >> >> >> Probe Set ID Gene Symbol Gene Title >> 244901_at ORF25 hypothetical protein >> 244902_at NAD4L NADH dehydrogenase subunit 4L >> 244912_at CCB382 cytochrome c biogenesis orf382 >> 244919_at CCB203 cytochrome c biogenesis orf203 >> 244925_at NAD7 NADH dehydrogenase subunit 7 >> >> How can I obtain the third column from biomart. I tried searching the >> attributes, but couldn't find the right name. Is it a matter of trial >> and error to find the correct attribute, or >> are there systematic ways to find it. Here is what I have so far: >> >> library("biomaRt") >> probeSets <- c("219666_at", "220547_s_at", "218034_at") >> >> ensembl = useMart("ensembl") >> ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl) >> >> idens <- getBM(attributes = c("affy_hg_u133a","hgnc_symbol"), filters >> = "affy_hg_u133a",values = probeSets, mart = ensembl) >> >> >> Also, does anyone have any suggestions regarding how to handle the >> duplicates (seen in this example) with respect to GSEA. >> >> Thanks, >> >> Juliet Hannah >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >