I am having a bit of trouble getting an MAplot from a result subset (though ?plotMA says this is possible) of a DESeq2 dataset. I am doing the following and getting this error:
> plotMA(BN_group_female_padj.01, alpha = .01, contrast=c("group", "femaleBB", "femalevehicle") ,ylim=c(-10,10)) Error in plotMA(BN_group_female_padj.01, alpha = 0.01, contrast = c("group", : Error from the generic function 'plotMA' defined in package 'BiocGenerics': no S4 method definition for argument 'BNST_group_female_padj.01' of class 'GRanges' was found. Did you perhaps mean calling the function 'plotMA' from another package, e.g. 'limma'? In that case, please use the syntax 'limma::plotMA'.
I can plot it from the entirety of the DEseqDataSet however I can't seem to find a way to only plot sites below a specific padj?