[BioC] code not shown in EdgeR manual.

[James W. MacDonald]

Hi Son,

That's the old way of doing things. These days you can just do

y <- estimateDisp(y, design)

And I think the code is not shown there because it has been shown many 
times prior to that point in the document, and doesn't really change 
unless you have some reason to change from the default arguments.

Best,

Jim

On Thursday, March 06, 2014 6:16:24 AM, Son Pham wrote:
> Hi EdgeR community:
> I'm reading the edgeR
> manual<http://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf>
>   and
> have a question:
> In example page 31:
> "3.5 Comparisons Both Between and Within Subjects"
> After estimating the dispersions (*code not shown*), we can fit a linear
> model: ....
>
> Should the "*code not shown" *in this case be:
>
>> y <- estimateGLMCommonDisp(y,design)
>> y <- estimateGLMTrendedDisp(y,design)
>> y <- estimateGLMTagwiseDisp(y,design)
> Thank you!
> Son.
>
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>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099