[BioC] DEXSeq - identical p-values for all exons in a gene

KP [guest] guest at bioconductor.org
Thu Jan 16 23:48:11 CET 2014

Hi All, 

I have been running DEXSeq successfully on my dataset using the default, in-built linear models, but have been repeatedly running into problems when attempting to add an extra 'blocking' term to the model.

I have checked the vignette and I thought my usage was correct:  

formulaFullModel <- ~ sample + exon + libType:exon + condition:exon
formulaReducedModel <- ~ sample + exon + libType:exon

ecs <- read.HTSeqCounts(countfiles=countFiles, design=sampleTable, flattenedfile=annotationfile)
ecs <- estimateSizeFactors(ecs)
ecs <- estimateDispersions(ecs, formula=formulaFullModel, nCores=cores, quiet=FALSE, file='dexseq_progress_report.txt')
ecs<- fitDispersionFunction(ecs)

ecs <- testForDEU(ecs, formula0=formulaReducedModel, formula1=formulaFullModel, nCores=cores, quiet=FALSE, file='testforDEU_progress_report.txt')

To check whether my problem was related to the extra term or just manually specifying the model, I ran DEXSeq using only a basic model (no additional terms: formulaFullModel <- ~ sample + exon + condition:exon
formulaReducedModel <- ~ sample + exon ), and had the same problem. This suggests it must be something to do with how I am specifying the model or providing it to the functions...?  

This is the sample table setup for the basic model:

      X     countFile condition
1    H1   H.r1.counts   control
2    M1   M.r1.counts   treated
3  H2ac H.r2ac.counts   control
4  M2ac M.r2ac.counts   treated
5 Hshap   H.NA.counts   control
6 Mshap   M.NA.counts   treated

I assume the cause is something silly on my part but I am stumped.  Any help would be greatly appreciated!


P.S. I also tried running the pasilla dataset in the same way but that time it worked, normal p-values.

 -- output of sessionInfo(): 

Sorry but this session info might not be quite right - the original run was done on a server and the workspace was saved and opened in RStudio. This is the session info from RStudio.

R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)

 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C               LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
 [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8    LC_PAPER=en_AU.UTF-8       LC_NAME=C                 

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

other attached packages:
[1] BiocInstaller_1.12.0 DEXSeq_1.8.0         Biobase_2.22.0       BiocGenerics_0.8.0  

loaded via a namespace (and not attached):
 [1] biomaRt_2.18.0       Biostrings_2.30.1    bitops_1.0-6         GenomicRanges_1.14.4 hwriter_1.3         
 [6] IRanges_1.20.6       RCurl_1.95-4.1       Rsamtools_1.14.2     statmod_1.4.18       stats4_3.0.2        
[11] stringr_0.6.2        tools_3.0.2          XML_3.98-1.1         XVector_0.2.0        zlibbioc_1.8.0      

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