On 02/13/2011 07:00 PM, Dario Strbenac wrote: > Hi, > > We've noticed that using runmean on Rles with all elements being a mix of > positive or zero numbers sometimes results in some very small negative > numbers. Is it possible for it to be exactly zero ? > >> cvg > 'numeric' Rle of length 199432144 with 1495580 runs > Lengths: 35100 35 ... 18 > Values : 0 0.750447078847223 ... 0.750447078847223 >> negs <- which(cvg < 0) >> negs > integer(0) >> smCvg <- IRanges::runmean(cvg, 1001, endrule = "constant") >> negs <- which(smCvg < 0) >> smCvg[head(negs)] > 'numeric' Rle of length 6 with 1 run > Lengths: 6 > Values : -1.56163238628593e-16
Not that there couldn't be improvements in numerical precision of runmean, but this is a realization of R FAQ 7.31 http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f See also ?signif. Martin > >> sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 > [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] aroma.affymetrix_1.7.0 aroma.apd_0.1.7 > [3] affxparser_1.22.0 R.huge_0.2.0 > [5] aroma.core_1.7.0 aroma.light_1.18.0 > [7] matrixStats_0.2.2 R.rsp_0.4.0 > [9] R.cache_0.3.0 R.filesets_0.9.0 > [11] digest_0.4.2 R.utils_1.5.3 > [13] R.oo_1.7.4 R.methodsS3_1.2.1 > [15] BSgenome.Hsapiens.UCSC.hg18_1.3.16 BSgenome_1.18.3 > [17] Biostrings_2.18.2 GenomicRanges_1.2.3 > [19] IRanges_1.8.9 > > loaded via a namespace (and not attached): > [1] Biobase_2.10.0 tools_2.12.0 > > > > -------------------------------------- > Dario Strbenac > Research Assistant > Cancer Epigenetics > Garvan Institute of Medical Research > Darlinghurst NSW 2010 > Australia > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
