For those people encounter the same problem like me.
plotMA in R and check the working environment. For example, I got
> plotMA function (object, ...) UseMethod("plotMA") <environment: namespace:limma>
It means the
plotMA() I used isn’t DESeq2’s plotMA function. In this situation, use
DESeq2::plotMA() instead of
plotMA() to make MA plot.
It looks like your model lacked an intercept and you didn't specify a contrast. You'll need to show the full set of commands (specifically, how you made your original DESeqDataset and the contents of any sample sheet involved). Also, you'll need to post the output of