[BioC] EdgeR: dispersion estimation

[Yanzhu [guest]]

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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