in the simple annotation objects chr entries should be the original chr numbers or indices into chrMap? in your withShortRead example THRO55C.1 had VIII translated to 8 in the simple annotation form when in chrMap it has location 13 in chrMap. thank you Nitzan -- output of sessionInfo(): R version 2.11.0 (2010-04-22) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 [5] LC_MONETARY=C LC_MESSAGES=en_US.iso885915 [7] LC_PAPER=en_US.iso885915 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] Genominator_1.2.0 GenomeGraphs_1.8.0 biomaRt_2.4.0 [4] RSQLite_0.9-1 DBI_0.2-5 ShortRead_1.6.2 [7] Rsamtools_1.0.8 lattice_0.18-5 Biostrings_2.16.9 [10] GenomicRanges_1.0.9 IRanges_1.6.17 loaded via a namespace (and not attached): [1] Biobase_2.8.0 hwriter_1.3 RCurl_1.6-10 tools_2.11.0 XML_3.4-3 -- Sent via the guest posting facility at bioconductor.org.

Nitzan, You are talking about the annotation data.frame? Yes, you need the chromosome names to be integers. If you have a chromosome map you can fix this by anno$chr <- match(anno$old_chr, chrMap) Kasper On Thu, Nov 17, 2011 at 4:10 AM, nitzan kol [guest] <guest at="" bioconductor.org=""> wrote: > > in the simple annotation objects chr entries should be the original chr numbers or indices into chrMap? > in your withShortRead example THRO55C.1 had VIII translated to 8 in the simple annotation form when in chrMap it has location 13 in chrMap. > > ?thank you > Nitzan > > ?-- output of sessionInfo(): > > R version 2.11.0 (2010-04-22) > x86_64-unknown-linux-gnu > > locale: > ?[1] LC_CTYPE=en_US.iso885915 ? ? ? LC_NUMERIC=C > ?[3] LC_TIME=en_US.iso885915 ? ? ? ?LC_COLLATE=en_US.iso885915 > ?[5] LC_MONETARY=C ? ? ? ? ? ? ? ? ?LC_MESSAGES=en_US.iso885915 > ?[7] LC_PAPER=en_US.iso885915 ? ? ? LC_NAME=C > ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? ? ? LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C > > attached base packages: > [1] grid ? ? ?stats ? ? graphics ?grDevices utils ? ? datasets ?methods > [8] base > > other attached packages: > ?[1] Genominator_1.2.0 ? GenomeGraphs_1.8.0 ?biomaRt_2.4.0 > ?[4] RSQLite_0.9-1 ? ? ? DBI_0.2-5 ? ? ? ? ? ShortRead_1.6.2 > ?[7] Rsamtools_1.0.8 ? ? lattice_0.18-5 ? ? ?Biostrings_2.16.9 > [10] GenomicRanges_1.0.9 IRanges_1.6.17 > > loaded via a namespace (and not attached): > [1] Biobase_2.8.0 hwriter_1.3 ? RCurl_1.6-10 ?tools_2.11.0 ?XML_3.4-3 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 >