Dear Rhoda & Teresa thanks! That clarifies - the two query results are linked by "ensembl_gene_id". There is no need to open two different connections in biomaRt, so example code including merging and some clean up could look like: library("biomaRt") mart = useMart("ensembl") ensembl = useDataset("hsapiens_gene_ensembl", mart = mart) p = c("200641_s_at" , "229411_at" , "223376_s_at") Q1 = getBM(attributes = c("affy_hg_u133_plus_2","entrezgene","ensembl_gene_id"), filters = "affy_hg_u133_plus_2", mart=ensembl, values=p) Q2 = getBM(attributes=c("validated","ensembl_gene_id"), filters="affy_hg_u133_plus_2", mart=ensembl, values=p) ## clean up: ## Q1 = subset(Q1, !is.na(entrezgene)) Q = merge(Q1,Q2) Best wishes Wolfgang ---------------------------------------------------- Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber Rhoda Kinsella wrote: > Hi Wolfgang and Teresa, > In the query below, Q1 and Q2 are still accessing the same mart > (mart=ensembl) so this will try to get the attributes from multiple > pages of the same mart. You will need to set up two distinct mart > datasets (mart1 and mart2) and as Ensembl is gene centric, you will also > have to include something for the two datasets to link on (e.g. Ensembl > gene ID or Ensembl transcript ID as these are present on the two pages > that you are trying to access). I think you need to do something like this: > > > library(biomaRt) > > mart1 = useMart("ensembl") > > mart2 = useMart("ensembl") > > ensembl1 = useDataset("hsapiens_gene_ensembl",mart=mart1); > Checking attributes and filters ... ok > > ensembl2 = useDataset("hsapiens_gene_ensembl",mart=mart2); > Checking attributes and filters ... ok > > getBM(attributes=c("affy_hg_u133_plus_2","entrezgene", > "ensembl_gene_id"), > filters="affy_hg_u133_plus_2",mart=ensembl1,values="205953_at"); > > affy_hg_u133_plus_2 entrezgene ensembl_gene_id > 1 205953_at 9860 ENSG00000198799 > > > getBM(attributes=c("validated", > "ensembl_gene_id"),filters="affy_hg_u133_plus_2",mart=ensembl2, > values="205953_at"); > validated ensembl_gene_id > 1 ENSG00000198799 > 2 hapmap ENSG00000198799 > 3 cluster,freq,submitter,doublehit,hapmap ENSG00000198799 > 4 freq,hapmap ENSG00000198799 > 5 cluster,freq,submitter,hapmap ENSG00000198799 > 6 freq,doublehit,hapmap ENSG00000198799 > 7 cluster,doublehit ENSG00000198799 > 8 cluster ENSG00000198799 > 9 cluster,freq,hapmap ENSG00000198799 > 10 cluster,freq,doublehit,hapmap ENSG00000198799 > 11 cluster,freq,doublehit ENSG00000198799 > 12 freq ENSG00000198799 > 13 doublehit ENSG00000198799 > 14 cluster,hapmap ENSG00000198799 > 15 freq,submitter,hapmap ENSG00000198799 > > I am sure that there is a more elegant way of doing the linking using > biomaRt. I hope this helps but if anything is not clear, please don't > hesitate to get in touch. > Regards, > Rhoda > > >> Dear Rhoda, Teresa >> >> if I try that suggestion, by: >> >> >> library("biomaRt") >> mart = useMart("ensembl") >> ensembl = useDataset("hsapiens_gene_ensembl", mart = mart); >> >> library("hgu133plus2.db") >> EID = toTable(hgu133plus2ENTREZID) >> set.seed(0xbadbeef) >> I = sample(nrow(EID), 100) >> p = EID[I,"probe_id"] >> >> Q1=getBM(attributes=c("affy_hg_u133_plus_2","entrezgene"),filters=" affy_hg_u133_plus_2",mart=ensembl,values=p) >> Q2=getBM(attributes=c("affy_hg_u133_plus_2","validated"),filters="a ffy_hg_u133_plus_2",mart=ensembl,values=p) >> >> >> I get: >> >> Error in getBM(attributes = c("affy_hg_u133_plus_2", "validated"), >> filters = "affy_hg_u133_plus_2", : >> Query ERROR: caught BioMart::Exception::Usage: Attributes from >> multiple attribute pages are not allowed >> >> >> (Note that this is the same error that Teresa encountered, just that >> in more recent versions of biomaRt the error message is more informative.) >> >> OTOH, if I only do >> >> Q3=getBM(attributes=c("validated"),filters="affy_hg_u133_plus_2",ma rt=ensembl,values=p) >> >> this returns successfully, but then Q3 has 27 rows and there seems no >> way to find out to which of the filter values the rows belong to - >> i.e., it is useless. >> >> So what's the best way to proceed when one wants to query across >> multiple pages like in Teresa's example? >> >> Best wishes >> Wolfgang >> >> ---------------------------------------------------- >> Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber >> >> >> > sessionInfo() >> R version 2.10.0 Under development (unstable) (2009-04-02 r48271) >> x86_64-unknown-linux-gnu >> >> locale: >> LC_CTYPE=C;LC_NUMERIC=C;LC_TIME=C;LC_COLLATE=C;LC_MONETARY=C;LC_MES SAGES=la_AU.UTF-8;LC_PAPER=C;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_ MEASUREMENT=C;LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices datasets utils methods base >> >> other attached packages: >> [1] hgu133plus2.db_2.2.11 RSQLite_0.7-1 DBI_0.2-4 >> [4] AnnotationDbi_1.5.23 Biobase_2.3.11 biomaRt_1.99.8 >> [7] fortunes_1.3-6 >> >> loaded via a namespace (and not attached): >> [1] RCurl_0.94-1 XML_2.3-0 >> >> >> >> Rhoda Kinsella wrote: >>> Hi Teresa, >>> The Ensembl mart attributes are set up as 4 separate categories or >>> "pages". If you take a look at the martview interface you will see >>> that these categories are: Features, Homologs, Structures, Sequences >>> and Variations. At present, it is not possible to mix attributes from >>> multiple sections as you will get the error message you received >>> (i.e. in your query the "validated" attribute came from the >>> "Variations" section and the rest of the attributes came from the >>> "Features" section). The way around this is to perform two separate >>> queries; one to select the features attributes and one to retrieve >>> the variations attribute. You may also be able to link to two >>> separate datasets, one for the validated part of the query and the >>> other for the features part of the query and pull out all the >>> information you need. I'm not sure how this is done using biomaRt, >>> but perhaps someone else from the mailing list can help you to do this. >>> I hope that helps, >>> Regards, >>> Rhoda >>> On 3 Apr 2009, at 15:09, Teresa Colombo wrote: >>>> Dear list, >>>> >>>> it looks like there may be a bug in function 'getBM' affecting the >>>> use of >>>> attribute 'validated': >>>> >>>> ----------------------------------------------------------------- --------------------------------------------------- >>>> >>>>> library(biomaRt) >>>>> mart = useMart("ensembl") >>>>> ensembl = useDataset("hsapiens_gene_ensembl", mart = mart); >>>> >>>>> library(hgu133plus2.db); >>>>> EID <- toTable(hgu133plus2ENTREZID); >>>>> I <- sample(dim(EID)[1],100) >>>>> p <- EID[I,"probe_id"]; >>>>> head(p) >>>> [1] "205953_at" "214718_at" "233633_at" "241572_at" "224704_at" >>>> [6] "221510_s_at" >>>> >>>> >>>>> Q <- >>>> getBM(attributes=c("affy_hg_u133_plus_2","entrezgene","validated" ),filters="affy_hg_u133_plus_2",mart=ensembl,values=p); >>>> >>>> >>>> V1 >>>> 1 Query ERROR: caught BioMart::Exception::Usage: Attributes from >>>> multiple >>>> attribute pages are not allowed >>>> Errore in getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene", >>>> "validated"), : >>>> Number of columns in the query result doesn't equal number of attributes >>>> in query. This is probably an internal error, please report. >>>> >>>> >>>> ----------------------------------------------------------------- --------------------------------------------------- >>>> >>>> The above error message disappears when running the same query after >>>> having >>>> removed "validated" from the list of attributes. >>>> ----------------------------------------------------------------- --------------------------------------------------- >>>> >>>>> Q <- >>>> getBM(attributes=c("affy_hg_u133_plus_2","entrezgene"),filters="a ffy_hg_u133_plus_2",mart=ensembl,values=p); >>>> >>>>> head(Q) >>>> affy_hg_u133_plus_2 entrezgene >>>> 1 1552538_a_at NA >>>> 2 1552538_a_at 221458 >>>> 3 1554485_s_at 140738 >>>> 4 1555097_a_at 5737 >>>> 5 1564015_at NA >>>> 6 1564198_a_at 118611 >>>> >>>> >>>>> sessionInfo() >>>> R version 2.8.1 (2008-12-22) >>>> i486-pc-linux-gnu >>>> >>>> locale: >>>> LC_CTYPE=it_IT.UTF-8;LC_NUMERIC=C;LC_TIME=it_IT.UTF-8;LC_COLLATE= it_IT.UTF-8;LC_MONETARY=C;LC_MESSAGES=it_IT.UTF-8;LC_PAPER=it_IT.UTF-8 ;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=it_IT.UTF-8;LC_I DENTIFICATION=C >>>> >>>> >>>> attached base packages: >>>> [1] tools stats graphics grDevices utils datasets methods >>>> [8] base >>>> >>>> other attached packages: >>>> [1] hgu133plus2.db_2.2.5 RSQLite_0.7-1 DBI_0.2-4 >>>> [4] AnnotationDbi_1.4.3 Biobase_2.2.2 biomaRt_1.16.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] RCurl_0.94-1 XML_2.1-0 >>>> ----------------------------------------------------------------- --------------------------------------------------- >>>> >>>> >>>> >>>> Best wishes >>>> teresa >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch <mailto: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 >>> Rhoda Kinsella Ph.D. >>> Ensembl Bioinformatician, >>> European Bioinformatics Institute (EMBL-EBI), >>> Wellcome Trust Genome Campus, >>> Hinxton >>> Cambridge CB10 1SD, >>> UK. > > Rhoda Kinsella Ph.D. > Ensembl Bioinformatician, > European Bioinformatics Institute (EMBL-EBI), > Wellcome Trust Genome Campus, > Hinxton > Cambridge CB10 1SD, > UK. >