[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)

 [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            

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        



More information about the Bioconductor mailing list