Dear Community,

Sorry if this question is too simple. Would like to how to use plotMA to plot the unshrunken log2 fold changes in result table after calling, results(dds, addMLE=TRUE)  ? Many thanks.

Stephen

In the Details of ?plotMA

This function is essentially two lines of code: building a
‘data.frame’ and passing this to the ‘plotMA’ method for
‘data.frame’ from the geneplotter package. The code of this
function can be seen with: ‘getMethod("plotMA","DESeqDataSet")’ If
users wish to modify the graphical parameters of the plot, it is
recommended to build the data.frame in the same manner and call
‘plotMA’.

So you can just do:

plotMA(data.frame(res$baseMean, res$lfcMLE, res$padj < .1))