[BioC] error in DEXSeq fitDispersionFunction()
Georg Otto
gwo at well.ox.ac.uk
Tue Nov 29 15:30:21 CET 2011
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
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