[BioC] EdgeR: dispersion estimation
Yanzhu [guest]
guest at bioconductor.org
Wed Apr 23 16:58:30 CEST 2014
Dear community,
I use edgeR to do the data analysis of my RNA-seq project (as mentioned in my previous posts about multi-factor analysis of RNA-Seq project), I meet an issue with dispersion estimation:
I first used estimateGLMCommonDisp and then used estimateGLMTagwiseDisp to estimate the dispersion, however, I got 3.999943 for y$common.dispersion and 0.0624991 for all of the y$tagwise.dispersion (all of the y$tagwise.dispersion are the same). isn't it that all of the tagwise dispersion should NOT be the same?
The fellowing is the code I used:
##Read in count data
T<-data.frame(HTSeqRE)
##Factors:
Design<-data.frame(HTSeqCondRE[,2:4])
Rep<-as.factor(Design$Rep)
Line<-as.factor(Design$Line)
Sex<-as.factor(Design$Sex)
design<-model.matrix(~Line+Rep+Sex+Line:Rep+Line:Sex+Rep:Sex+Line:Sex:Rep)
group<-paste(Design$Line,Design$Sex,Design$Rep,sep=".")
y<-DGEList(counts=T,group=group)
y<-calcNormFactors(y,method="TMM")
y<-estimateGLMCommonDisp(y,design)
y<-estimateGLMTagwiseDisp(y,design)
y$common.dispersion
[1] 3.999943
y$tagwise.dispersion
[1] 0.0624991 0.0624991 0.0624991 0.0624991 0.0624991
13474 more elements ...
Yanzhu
-- output of sessionInfo():
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] DESeq_1.12.1 lattice_0.20-27 locfit_1.5-9.1 Biobase_2.20.1 BiocGenerics_0.6.0 edgeR_3.2.4 limma_3.16.8
loaded via a namespace (and not attached):
[1] annotate_1.38.0 AnnotationDbi_1.22.6 DBI_0.2-7 genefilter_1.42.0 geneplotter_1.38.0 grid_3.0.1 IRanges_1.18.4
[8] RColorBrewer_1.0-5 RSQLite_0.11.4 splines_3.0.1 stats4_3.0.1 survival_2.37-4 tools_3.0.1 XML_3.98-1.1
[15] xtable_1.7-3
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