[BioC] estimateGLMCommonDisp and dispCoxReid in edgeR

[Gordon K Smyth]

Sorry, that should be "Dear Wade".

One of the authors of the estimateGLMCommonDisp() is Davis McCarthy, so 
I've got used to "Davis" being a first name.

Best wishes
Gordon



On Wed, 14 Dec 2011, Gordon K Smyth wrote:

> 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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