Hi All,

I am trying to use DEXSeq to find out differential exon usage and encounter the following error. I have included the session info and my R script. 

Could you please help me finding out what could be the problem?


Estimating Cox-Reid exon dispersion estimates using 30 cores. (Progress report: one dot per 100 genes)
........................................................................................................................Testing for differential exon usage using 30 cores. (Progress report: one dot per 100 genes)
........................................................................................................................Error in pmax(which(decade_lengths > 0.1), 0) : 
  cannot mix 0-length vectors with others

The session info is below.
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] DEXSeq_1.2.0       Biobase_2.16.0     BiocGenerics_0.2.0 multicore_0.1-7   

loaded via a namespace (and not attached):
[1] RCurl_1.91-1   XML_3.9-4      biomaRt_2.12.0 hwriter_1.3    plyr_1.7.1    
[6] statmod_1.4.14 stringr_0.6   
> 

My R script is below:
$ more run-FL-LL-12-fdr-0.05.R 
library(multicore)
library(DEXSeq)
annotationfile = file.path("Gallus_gallus.WASHUC2.64.clc.gff")
samples = data.frame(
	condition = c(rep("FL", 12), rep("LL", 12)),
	replicate = c(1:12, 1:12),
	row.names = dir("clcExonCountFiles", full.names=TRUE, pattern=".count"),
	stringsAsFactors = TRUE,
	check.names = FALSE
)
ecs = read.HTSeqCounts(countfiles = file.path(rownames(samples)), design = samples, flattenedfile = annotationfile)
ecs = estimateSizeFactors(ecs)
ecs = estimateDispersions(ecs, nCores=30)
ecs = fitDispersionFunction(ecs)
ecs = testForDEU(ecs, nCores=30)
DEXSeqHTML(ecs, geneIDs=NULL, path="report/FL-LL-12/FDR-0.05", file = "FL-LL-DEU-fdr0.05.html", fitExpToVar="condition", FDR=0.05, color=NULL, color.samples=NULL)
	[[alternative HTML version deleted]]

