[BioC] GLM in DEseq

[Simon Anders]

>   How can I retrieve the coefficients corresponding to the contribution of each factor (ie effect due to genotype, due to treatment and the interaction between genotype and treatment) ?

Have a look into the data frame returned by fitNbinomGLMs. They contain 
all the estimated coefficients, plus two further columns, one with the 
deviances and a booleant to inidicate convergence. (See also 
"?fitNbinomGLMs")

   Simon