[BioC] EdgeR: ANOVA-like analysis

[Gordon K Smyth]

Dear Christian,

limma syntax doesn't always work in edgeR.  We will work to make them as 
analogous as we can, but generalized linear models in edgeR bring in a few 
unavoidable complications into edgeR that are not present in limma.

At the moment, the contrast argument to glmLRT() must be a vector, not a 
matrix, as is explained on the help page for that function.  In future we 
will add the matrix capability, but for now you will need to perform 
F-test-like likelihood ratio tests using the coef argument instead.  This 
means that you must paramatrize your design matrix so that it contains an 
intercept column:

   design <- model.matrix(~group)

Then later you can use

   glmLRT(..., coef=2:4)

and so on.  This will do the combined test that you want on 3 df for 
differences between the 4 groups.

Best wishes
Gordon

> Date: Mon, 20 Jun 2011 11:12:39 -0300
> From: "Christian M. Probst" <cprobst at fiocruz.br>
> To: bioconductor at r-project.org
> Subject: [BioC] EdgeR: ANOVA-like analysis
>
> Dear list,
>
> I am using edgeR to analyze a RNA-Seq dataset consisting of 4 samples
> (groups), each with 5 biological replicates.
>
> I have read in the Limma manual, as it has an extensive description of
> design models. In section 8.6, there is a description for multiple groups
> test, and I have tried to follow the steps there. But the edgeR objects are
> distinct from the Limma, so I am stucked.
>
> Shortly, I want to use edgeR to identify differential expression in all
> pair-wise comparisons of the 4 groups, as well as combine all pair-wise
> comparisons into one F-test.
>
> I have used the following construction:
>
> deF<-glmLRT(dgecRNAF,glmFit(dgecRNAF, mmcRNA,
> dispersion=dgecRNAF$common.dispersion), contrast=contrast.matrix)
>
> where dgecRNAF is my DGEList object, mmcRNA is my model matrix, and
> contrast.matrix is:
>
>> contrast.matrix
>      Contrasts
> Levels    A-B   A-C   A-D   B-C   B-D   C-D
>   A       1     1     1     0     0     0
>   B      -1     0     0     1     1     0
>   C       0    -1     0    -1     0     1
>   D       0     0    -1     0    -1    -1
>
>
> Thanks in advance,
>
> -- 
> Dr. Christian Macagnan Probst
>
> Adjunct Researcher in Public Health
> Bioinformatics and Computational Biology Laboratory
> Functional Genomics Laboratory
>
> Carlos Chagas Institute - ICC/FIOCRUZ
> Curitiba - PR - Brasil
>
> Reseacher ID: http://www.researcherid.com/rid/B-8678-2009

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