[BioC] estimateGLMCommonDisp and dispCoxReid in edgeR

[Gordon K Smyth]

Dear Davis,

The dispCoxReid() function is a low-level function in edgeR that works 
directly on matrices rather than DGEList objects, and it's not intended to 
be called directly by users.

You get different results from dispCoxReid() because you have not passed 
to it the offsets based on library sizes and normalization. 
estimateGLMCommonDisp() extracts this information automatically from the 
object, but the low-level functions don't do this.

Best wishes
Gordon

---------------------------------------------
Professor Gordon K Smyth,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
Tel: (03) 9345 2326, Fax (03) 9347 0852,
smyth at wehi.edu.au
http://www.wehi.edu.au
http://www.statsci.org/smyth

On Tue, 13 Dec 2011, Davis, Wade wrote:

> 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
>

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