I tried splitting my initial query into two smaller ones taht are connected by a common attribute which is needed to recombine the information pieces together. I realized some combinations work fine whereas I get the same error in other cases: The following three queirs work > genes_map1 <- getBM(attributes=c("entrezgene","hgnc_symbol","ensembl _gene_id","ensembl_transcript_id"),filters = "entrezgene", values=genes.ds[1:36,1], mart=hmart) > genes_map2 <- getBM(attributes=c("ensembl_transcript_id","3_utr_start","3_utr_end"), + filters = "entrezgene", values=genes.ds[,1], mart=hmart) > genes_map3 <- getBM(attributes=c("ensembl_gene_id","3_utr_start","3_utr_end"), + filters = "entrezgene", values=genes.ds[1:36,1], mart=hmart) The following queries generate the same error > genes_map4 <- getBM(attributes=c("hgnc_symbol","3_utr_start","3_utr_end"), + filters = "entrezgene", values=genes.ds[1:36,1], mart=hmart) Error in getBM(attributes = c("hgnc_symbol", "3_utr_start", "3_utr_end"), : Query ERROR: caught BioMart::Exception::Usage: Attributes from multiple attribute pages are not allowed > genes_map4 <- getBM(attributes=c("entrezgene","3_utr_start","3_utr_end"), + filters = "entrezgene", values=genes.ds[1:36,1], mart=hmart) Error in getBM(attributes = c("entrezgene", "3_utr_start", "3_utr_end"), : Query ERROR: caught BioMart::Exception::Usage: Attributes from multiple attribute pages are not allowed Is there any description of the attribute pages ? Thank you very much, Maura tutti i telefonini TIM! [[alternative HTML version deleted]]

Hello Maude, have a look at the attributePages() function. That will tell you what kind of attributes are available for the mart connection you're using. In combination with listAttributes(..., page=), this will tell you what queries can be combined. Best \Heidi On 14 May 2010, at 14:15, <mauede at="" alice.it=""> <mauede at="" alice.it=""> wrote: > I tried splitting my initial query into two smaller ones taht are > connected by a common attribute which is needed to recombine the > information pieces together. > I realized some combinations work fine whereas I get the same error > in other cases: > > The following three queirs work >> genes_map1 <- getBM(attributes=c >> ("entrezgene","hgnc_symbol","ensembl_gene_id","ensembl_transcript_id" >> ),filters = "entrezgene", values=genes.ds[1:36,1], mart=hmart) >> genes_map2 <- getBM(attributes=c >> ("ensembl_transcript_id","3_utr_start","3_utr_end"), > + filters = "entrezgene", values=genes.ds[,1], mart=hmart) >> genes_map3 <- getBM(attributes=c >> ("ensembl_gene_id","3_utr_start","3_utr_end"), > + filters = "entrezgene", values=genes.ds[1:36,1], mart=hmart) > > The following queries generate the same error >> genes_map4 <- getBM(attributes=c >> ("hgnc_symbol","3_utr_start","3_utr_end"), > + filters = "entrezgene", values=genes.ds[1:36,1], mart=hmart) > Error in getBM(attributes = c("hgnc_symbol", "3_utr_start", > "3_utr_end"), : > Query ERROR: caught BioMart::Exception::Usage: Attributes from > multiple attribute pages are not allowed >> genes_map4 <- getBM(attributes=c >> ("entrezgene","3_utr_start","3_utr_end"), > + filters = "entrezgene", values=genes.ds[1:36,1], mart=hmart) > Error in getBM(attributes = c("entrezgene", "3_utr_start", > "3_utr_end"), : > Query ERROR: caught BioMart::Exception::Usage: Attributes from > multiple attribute pages are not allowed > > Is there any description of the attribute pages ? > Thank you very much, > Maura > > > > tutti i telefonini TIM! > > > [[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