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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