Hi, I get the following warning: library(GenomicFeatures) myDB <- makeTranscriptDbFromBiomart(biomart = "ensembl", dataset = "scerevisiae_gene_ensembl", circ_seqs = c(DEFAULT_CIRC_SEQS, "Mito")) Download and preprocess the 'transcripts' data frame ... OK Download and preprocess the 'chrominfo' data frame ... FAILED! (=> skipped) Download and preprocess the 'splicings' data frame ... OK Download and preprocess the 'genes' data frame ... OK Prepare the 'metadata' data frame ... OK Make the TranscriptDb object ... OK Warning message: In .normargChrominfo(chrominfo, transcripts$tx_chrom, splicings$exon_chrom) : chromosome lengths and circularity flags are not available for this TranscriptDb object > sessionInfo() R Under development (unstable) (2013-02-27 r62087) Platform: x86_64-unknown-linux-gnu (64-bit) 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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GenomicFeatures_1.11.16 AnnotationDbi_1.21.14 Biobase_2.19.3 [4] GenomicRanges_1.11.37 IRanges_1.17.37 BiocGenerics_0.5.6 loaded via a namespace (and not attached): [1] biomaRt_2.15.1 Biostrings_2.27.11 bitops_1.0-5 [4] BSgenome_1.27.1 DBI_0.2-5 RCurl_1.95-4.1 [7] Rsamtools_1.11.22 RSQLite_0.11.2 rtracklayer_1.19.10 [10] stats4_3.0.0 tools_3.0.0 XML_3.95-0.2 [13] zlibbioc_1.5.0 Is this an issue of GenomicFeatures or Ensembl? Best, Stefanie

Hi Stefanie, This is not an error but a warning. It means that the data resource you are extracting from does not indicate which chromosomes are circular/linear or how long the various chromosomes are. You have to decide if that matters to you or not. If it matters, then you might want to see the manual page for seqlengths() and isCircular() and consider settting that information manually. Marc On 03/15/2013 03:54 AM, Stefanie Tauber wrote: > Hi, > > I get the following warning: > > library(GenomicFeatures) > > myDB<- makeTranscriptDbFromBiomart(biomart = "ensembl", dataset = > "scerevisiae_gene_ensembl", circ_seqs = c(DEFAULT_CIRC_SEQS, "Mito")) > > Download and preprocess the 'transcripts' data frame ... OK > Download and preprocess the 'chrominfo' data frame ... FAILED! (=> skipped) > Download and preprocess the 'splicings' data frame ... OK > Download and preprocess the 'genes' data frame ... OK > Prepare the 'metadata' data frame ... OK > Make the TranscriptDb object ... OK > Warning message: > In .normargChrominfo(chrominfo, transcripts$tx_chrom, splicings$exon_chrom) : > chromosome lengths and circularity flags are not available for this > TranscriptDb object > > >> sessionInfo() > R Under development (unstable) (2013-02-27 r62087) > Platform: x86_64-unknown-linux-gnu (64-bit) > > 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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] GenomicFeatures_1.11.16 AnnotationDbi_1.21.14 Biobase_2.19.3 > [4] GenomicRanges_1.11.37 IRanges_1.17.37 BiocGenerics_0.5.6 > > loaded via a namespace (and not attached): > [1] biomaRt_2.15.1 Biostrings_2.27.11 bitops_1.0-5 > [4] BSgenome_1.27.1 DBI_0.2-5 RCurl_1.95-4.1 > [7] Rsamtools_1.11.22 RSQLite_0.11.2 rtracklayer_1.19.10 > [10] stats4_3.0.0 tools_3.0.0 XML_3.95-0.2 > [13] zlibbioc_1.5.0 > > > > Is this an issue of GenomicFeatures or Ensembl? > Best, > Stefanie > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor