Hello, It used to work half a year ago, but now I get an error message: > summary<-aggregate(simple.rle.list, IRanges.list, FUN=sum) Error in .local(x, ...) : for Ranges 'by', 'length(x) != length(by)' Basically, I want to sample the Rle vector at specific ranges and get sum of the values over the indicated ranges. Thank you for help, Skirmantas K. Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.12.0 RCurl_1.5-0 [3] bitops_1.0-4.1 BSgenome.Mmusculus.UCSC.mm9_1.3.17 [5] biomaRt_2.8.0 chipseq_1.2.0 [7] ShortRead_1.10.0 Rsamtools_1.4.0 [9] lattice_0.19-26 BSgenome_1.20.0 [11] Biostrings_2.20.0 GenomicRanges_1.4.1 [13] IRanges_1.10.0 loaded via a namespace (and not attached): [1] Biobase_2.12.1 grid_2.13.0 hwriter_1.3 tools_2.13.0 XML_3.2-0 [[alternative HTML version deleted]]

It looks to me like your RangesList and RleList are of different lengths -- do you have a simple self-contained example? Btw, I think you're better off doing this: viewSums(Views(simple.rle.list, IRanges.list)) But that won't work if you've got incompatible lists. Michael On Fri, Jun 10, 2011 at 5:47 AM, Skirmantas Kriaucionis < skirmantas.kriaucionis@ludwig.ox.ac.uk> wrote: > Hello, > > It used to work half a year ago, but now I get an error message: > > > summary<-aggregate(simple.rle.list, IRanges.list, FUN=sum) > Error in .local(x, ...) : for Ranges 'by', 'length(x) != length(by)' > > Basically, I want to sample the Rle vector at specific ranges and get sum > of the values over the indicated ranges. > > Thank you for help, > Skirmantas K. > > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] rtracklayer_1.12.0 RCurl_1.5-0 > [3] bitops_1.0-4.1 BSgenome.Mmusculus.UCSC.mm9_1.3.17 > [5] biomaRt_2.8.0 chipseq_1.2.0 > [7] ShortRead_1.10.0 Rsamtools_1.4.0 > [9] lattice_0.19-26 BSgenome_1.20.0 > [11] Biostrings_2.20.0 GenomicRanges_1.4.1 > [13] IRanges_1.10.0 > > loaded via a namespace (and not attached): > [1] Biobase_2.12.1 grid_2.13.0 hwriter_1.3 tools_2.13.0 XML_3.2-0 > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > [[alternative HTML version deleted]]