Hi, I want to retrieve some annotation informations from "ensembl exon id" by using a biomart query : "ensembl gene id", "ensembl transcript id", ... After my "getBM" query, without error message, my object "results" contains lot of "NA" values but if I re-send a query on "NA" values id, I successfully retrieve informations. Example : library(biomaRt) ensembl <- useMart(host="jan2013.archive.ensembl.org", biomart="ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl") results <- getBM(attributes=c("ensembl_exon_id","ensembl_gene_id"),fil ters="ensembl_exon_id",values=ENSE,mart=ensembl, uniqueRows=TRUE) My object ENSE contain 512120 exon_id. Why I obtain lot of "NA" values when my value option is large ? Must I to split it ? and Why ? Thanks, Elodie sessionInfo() R version 3.1.1 (2014-07-10) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C [3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8 [5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8 [7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.20.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.26.0 Biobase_2.24.0 BiocGenerics_0.10.0 [4] DBI_0.2-7 GenomeInfoDb_1.0.2 IRanges_1.22.9 [7] parallel_3.1.1 RCurl_1.95-4.1 RSQLite_0.11.4 [10] stats4_3.1.1 tools_3.1.1 XML_3.98-1.1 Elodie Chapeaublanc IE Bioinformatique Équipe Oncologie Moléculaire Institut Curie - UMR 144 - CNRS 26 rue d'Ulm - 75248 Paris Cedex 05 Tel: +33 1 56 24 63 57 Email: elodie.chapeaublanc@curie.fr _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor