Hi everyone, I have been playing with the biomaRt package a bit more and I am trying to work out what is going on here: ensembl = useMart("ensembl_mart_47", dataset = "hsapiens_gene_ensembl", archive = TRUE) fetched = getBM(c("affy_hg_u133_plus_2", "hgnc_symbol"), filters = c("chromosome_name", "start", "end"), values = list(as.numeric("9"), 19198907, 19357826), mart = ensembl) affy_hg_u133_plus_2 hgnc_symbol 1 226867_at 2 205684_s_at 3 226867_at DENND4C 4 205684_s_at DENND4C 5 234968_at 6 234968_at DENND4C fetched = getBM(c("affy_hg_u133_plus_2", "hgnc_symbol"), filters = c("chromosome_name", "start", "end"), values = list(as.numeric("9"), 33925736, 34088257), mart = ensembl) affy_hg_u133_plus_2 hgnc_symbol 1 2 224789_at 3 224789_at WDR40A I cannot understand why I am getting 2 rows for some probesets one containing a hugo identifier and the other not? And whether there is any relevance to this result ( probeset 234968_at ) and why I have some results which don't show any probeset at all? Is there a specific reason for this or is this just a something that needs to be post filtered? Many thanks in advance. Nathan

Hi, I basically want to return a list of probe, hugo identifier (or ""). I have just tried the line of code you suggested and I get the following error: Error in values[[i]] : subscript out of bounds So I'm afraid it doesnt work. Any ideas what the change to it should be? I tried: getBM(c("affy_hg_u133_plus_2", "hgnc_symbol"), filters = c("chromosome_name", "start", "end", "with_affy_hg_u133_plus_2"), values = list(9, 19198907, 19357826), mart = ensembl) getBM(c("affy_hg_u133_plus_2", "hgnc_symbol"), filters = c("chromosome_name", "start", "end", "affy_hg_u133_plus_2"), values = list(9, 19198907, 19357826), mart = ensembl) Any ideas? I couldn't find a description of how to change this behaviour in the vignette. Nathan 2008/8/17 Stephen Henderson <to.stephen.henderson at="" googlemail.com="">: > Hi > getBM is returning all genes (or transcripts??) within that area (i.e. > filters =...) including some that do not have affy probes for them. If you > wanted to see them then you would have to put more 'attributes' into the > getBM function e.g. > getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"),... > Alternatively if you wanted only those transcripts with affy ids then you > would need to specify this in the filters e.g. > fetched = getBM(c("affy_hg_u133_plus_2", "hgnc_symbol"), filters = > c("chromosome_name", "start", "end", "affy_hg_u133_plus_2"), values = > list(as.numeric("9"), > 19198907, 19357826), mart = ensembl) > The repeats are inherent to the ensembl database and arise for many reasons. > Stephen > > > > On 17 Aug 2008, at 20:23, Nathan Harmston wrote: > > Hi everyone, > > I have been playing with the biomaRt package a bit more and I am > trying to work out what is going on here: > > ensembl = useMart("ensembl_mart_47", dataset = > "hsapiens_gene_ensembl", archive = TRUE) > > fetched = getBM(c("affy_hg_u133_plus_2", "hgnc_symbol"), filters = > c("chromosome_name", "start", "end"), values = list(as.numeric("9"), > 19198907, 19357826), mart = ensembl) > affy_hg_u133_plus_2 hgnc_symbol > 1 226867_at > 2 205684_s_at > 3 226867_at DENND4C > 4 205684_s_at DENND4C > 5 234968_at > 6 234968_at DENND4C > > fetched = getBM(c("affy_hg_u133_plus_2", "hgnc_symbol"), filters = > c("chromosome_name", "start", "end"), values = list(as.numeric("9"), > 33925736, 34088257), mart = ensembl) > > affy_hg_u133_plus_2 hgnc_symbol > 1 > 2 224789_at > 3 224789_at WDR40A > > I cannot understand why I am getting 2 rows for some probesets one > containing a hugo identifier and the other not? And whether there is > any relevance to this result ( probeset 234968_at ) and why I have > some results which don't show any probeset at all? Is there a specific > reason for this or is this just a something that needs to be post > filtered? > > Many thanks in advance. > > Nathan > > _______________________________________________ > 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 Nathan, This how these BioMart systems work. If you do: fetched = getBM(c("affy_hg_u133_plus_2", "hgnc_symbol"), filters = c("chromosome_name", "start", "end", "with_hgnc_symbol"), values = list(as.numeric("9"),19198907, 19357826, TRUE), mart = ensembl) You'll only retrieve the affy ids once and each one of them will have an HGNC symbol. Cheers, Steffen > Hi everyone, > > I have been playing with the biomaRt package a bit more and I am > trying to work out what is going on here: > > ensembl = useMart("ensembl_mart_47", dataset = > "hsapiens_gene_ensembl", archive = TRUE) > > fetched = getBM(c("affy_hg_u133_plus_2", "hgnc_symbol"), filters = > c("chromosome_name", "start", "end"), values = list(as.numeric("9"), > 19198907, 19357826), mart = ensembl) > affy_hg_u133_plus_2 hgnc_symbol > 1 226867_at > 2 205684_s_at > 3 226867_at DENND4C > 4 205684_s_at DENND4C > 5 234968_at > 6 234968_at DENND4C > > fetched = getBM(c("affy_hg_u133_plus_2", "hgnc_symbol"), filters = > c("chromosome_name", "start", "end"), values = list(as.numeric("9"), > 33925736, 34088257), mart = ensembl) > > affy_hg_u133_plus_2 hgnc_symbol > 1 > 2 224789_at > 3 224789_at WDR40A > > I cannot understand why I am getting 2 rows for some probesets one > containing a hugo identifier and the other not? And whether there is > any relevance to this result ( probeset 234968_at ) and why I have > some results which don't show any probeset at all? Is there a specific > reason for this or is this just a something that needs to be post > filtered? > > Many thanks in advance. > > Nathan > > _______________________________________________ > 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 >