Question: error in DEXSeq fitDispersionFunction()
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gravatar for Georg Otto
8.0 years ago by
Georg Otto120
Georg Otto120 wrote:
Dear Bioconductors, I am trying to use DEXSeq to test for differential exon usage in my RNA-seq data. I was able to generate the exon count tables using the python scripts that come with the package and the function read.HTSeqCounts(). However, I get an error at this step: exon.counts <- fitDispersionFunction(exon.counts) Error in if (sum(log(coefs/oldcoefs)^2) < 0.005) break : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In glmgam.fit(mm, disps[good], start = coefs) : Too much damping - convergence tolerance not achievable 2: In log(coefs/oldcoefs) : NaNs produced Any idea what might be wrong here? Here is the output of sessionInfo() R version 2.13.0 (2011-04-13) 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] DEXSeq_1.0.1 DESeq_1.6.1 locfit_1.5-6 [4] lattice_0.19-26 akima_0.5-4 Biobase_2.14.0 [7] GenomicFeatures_1.4.4 GenomicRanges_1.4.8 IRanges_1.10.6 loaded via a namespace (and not attached): [1] annotate_1.30.0 AnnotationDbi_1.14.1 biomaRt_2.8.1 [4] Biostrings_2.20.1 BSgenome_1.20.0 DBI_0.2-5 [7] genefilter_1.34.0 geneplotter_1.30.0 grid_2.13.0 [10] hwriter_1.3 plyr_1.6 RColorBrewer_1.0-2 [13] RCurl_1.7-0 RSQLite_0.10.0 rtracklayer_1.12.4 [16] splines_2.13.0 statmod_1.4.14 stringr_0.5 [19] survival_2.36-9 tools_2.13.0 XML_3.4-3 [22] xtable_1.6-0 Cheers, Georg
dexseq • 475 views
ADD COMMENTlink written 8.0 years ago by Georg Otto120
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