How do you obtain the R - squared value from the NB line produced in plotMeanVar ?
plotMeanVar does not compute or output an R-square value.
This is not a correlation or regression problem, so R-square doesn't seem very relevant to me. It's not appropriate to measure lack of fit of variances around the trend lines by least squares. However plotMeanVar outputs the quantities shown on the plot, so you can easily compute any correlation you would like yourself.
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version 2.3.6
In the output of plotMeanVar, which values represent the NBline and the Poisson line? I see the Means and Vars, the avemeans and avevars, and the bin.means and bin.vars.
The lines arise from equations, not from vectors of estimates. The Poisson line in particular is obviously just the 1-1 line.
I am puzzled what you're trying to do. If you are trying to assess the adequacy of a Poisson model instead of negative binomial, then R-square is not the way to do it.