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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