Dear Hans, thank you very much for your feedback. Now everything is working! best r On 6 September 2010 12:20, Hans-Rudolf Hotz wrote: > René > > Have you tried again in the meantime, as this looks more like a temporary > glitch on the biomart backend? > > ie it works form me: > > > > library("biomaRt") > > mart = useMart("ensembl") > > ensembl = useDataset("hsapiens_gene_ensembl", mart=mart) > Checking attributes ... ok > Checking filters ... ok > > EGsub = c("1635_at"="25", "39329_at"="87", "40797_at"="102") > > utr = getSequence(id=EGsub, seqType="3utr", mart=ensembl, > type="entrezgene") > > > > utr['entrezgene'] > entrezgene > 1 25 > 2 102 > 3 25 > 4 87 > > > > (although, I am not quite sure, what you are trying to fetch from biomart) > > > regards, Hans > > > > > > sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.4.0 > > > loaded via a namespace (and not attached): > [1] RCurl_1.4-3 XML_3.1-1 > > > > > > > > On 09/06/2010 10:58 AM, René Dreos wrote: > >> Dear BioC mailing-list, >> >> I came across this error using the latest R version and BioMart: >> >> library("biomaRt") >>> mart = useMart("ensembl") >>> ensembl = useDataset("hsapiens_gene_ensembl", mart=mart) >>> >> Checking attributes ... ok >> Checking filters ... ok >> >>> EGsub = c("1635_at"="25", "39329_at"="87", "40797_at"="102") >>> utr = getSequence(id=EGsub, seqType="3utr", mart=ensembl, >>> >> type="entrezgene") >> >> V1 >> 1> Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> >> 2> HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1"> >> 3 >> ERROR: The requested URL could not be retrieved >> 4 >> 5 >> >> 6 >>

ERROR

>> Error in getBM(c(seqType, type), filters = type, values = id, mart = mart, >> : >> The query to the BioMart webservice returned an invalid result: the >> number >> of columns in the result table does not equal the number of attributes in >> the query. Please report this to the mailing list. >> >> I looked through the BioC mailing-list for similar errors but found only >> one >> quite similar last year. It was related to a bug in BioMart. Is this the >> same? >> >> Here is my session-info: >> >>> sessionInfo() >>> >> R version 2.11.1 (2010-05-31) >> x86_64-apple-darwin9.8.0 >> >> locale: >> [1] C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] RCurl_1.4-2 >> [2] bitops_1.0-4.1 >> [3] ChIPpeakAnno_1.4.1 >> [4] limma_3.4.4 >> [5] org.Hs.eg.db_2.4.1 >> [6] GO.db_2.4.1 >> [7] RSQLite_0.9-2 >> [8] DBI_0.2-5 >> [9] AnnotationDbi_1.10.2 >> [10] BSgenome.Ecoli.NCBI.20080805_1.3.16 >> [11] multtest_2.5.14 >> [12] Biobase_2.8.0 >> [13] biomaRt_2.4.0 >> [14] chipseq_0.4.1 >> [15] ShortRead_1.6.2 >> [16] Rsamtools_1.0.8 >> [17] lattice_0.18-8 >> [18] BSgenome.Athaliana.TAIR.04232008_1.3.16 >> [19] BSgenome_1.16.5 >> [20] Biostrings_2.16.9 >> [21] GenomicRanges_1.0.8 >> [22] IRanges_1.6.15 >> >> loaded via a namespace (and not attached): >> [1] MASS_7.3-6 XML_3.1-1 grid_2.11.1 hwriter_1.2 >> [5] splines_2.11.1 survival_2.35-8 tcltk_2.11.1 tools_2.11.1 >> >> >> Thank you very much for any feed-back, >> >> best >> r >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > [[alternative HTML version deleted]]