[BioC] estimateGLMCommonDisp and dispCoxReid in edgeR

[Davis, Wade]

Dear Mark, Gordon, and fellow BioConductoRs:

First, thank you for numerous contributions to the BioConductor project, and more broadly, to the statistics community.

I was curious if I should expect the same result from the two calls below. >From looking at the contents of estimateGLMCommonDisp.default, I think so, but I may be missing something with the default values that are passed into dispCoxReid from estimateGLMCommonDisp.

dge.ctl.filt <- estimateGLMCommonDisp(y=dge.ctl.filt, design=ctl.design,method="CoxReid") dge.ctl.filt$common.dispersion
 [1] 0.02058129

names(dge.ctl.filt)
[1] "samples"           "counts"            "all.zeros"         "common.dispersion"

dispCoxReid(y=dge.ctl.filt, design=ctl.design)
 [1] 0.2124361

My design matrix is nearly identical to the vignette example on Tuch's data (paired), but with one more subject.


ctl.design
      int id.2172 id.2186 id.2234 id.2244 Trt
 [1,]   1       1       0       0       0   0
 [2,]   1       1       0       0       0   1
 [3,]   1       0       0       0       1   0
 [4,]   1       0       0       0       1   1
 [5,]   1       0       0       1       0   0
 [6,]   1       0       0       1       0   1
 [7,]   1       0       1       0       0   0
 [8,]   1       0       1       0       0   1
 [9,]   1       0       0       0       0   0
[10,]   1       0       0       0       0   1
attr(,"assign")
[1] 0 1 1 1 1 2
attr(,"contrasts")
attr(,"contrasts")$`factor(cowID.ctl)`
[1] "contr.treatment"

attr(,"contrasts")$`dge.ctl.filt$samples$group`
[1] "contr.treatment"

Thanks for your attention. My session info is below.
Wade


> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
[1] limma_3.10.0 edgeR_2.4.1