Is there any simple way to extract the degrees of freedom from a
DESeqDataSet object that's been through the complete
At first I thought perhaps the empirical Bayes shrinkage augmented the df as it does in
limma, but that doesn't appear to be the case judging by the Love et al., 2014 paper. (Still not 100% certain about this.) Then I thought I could just subtract the number of coefficients from the number of samples as you would for any regular regression, but I'm a little confused by the talk of expanded model matrices in the documentation for
nbinomWaldTest. It sounds like the default behaviour of the function is to compute coefficients for each level of each factor, in addition to a model intercept. Does that mean that a simple control vs. treatment
DESeq analysis for a 10-sample experiment would have 7 degrees of freedom?