[BioC] DEXSeq - identical p-values for all exons in a gene
guest at bioconductor.org
Thu Jan 16 23:48:11 CET 2014
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 <- 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)
 LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
 LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 LC_PAPER=en_AU.UTF-8 LC_NAME=C
 LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
 parallel stats graphics grDevices utils datasets methods base
other attached packages:
 BiocInstaller_1.12.0 DEXSeq_1.8.0 Biobase_2.22.0 BiocGenerics_0.8.0
loaded via a namespace (and not attached):
 biomaRt_2.18.0 Biostrings_2.30.1 bitops_1.0-6 GenomicRanges_1.14.4 hwriter_1.3
 IRanges_1.20.6 RCurl_1.95-4.1 Rsamtools_1.14.2 statmod_1.4.18 stats4_3.0.2
 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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