​hi David,

I'm adding the Bioconductor mailing list to my response in case other
user's find the same error.

Plotting the object res returned by results() is demonstrated in the
vignette of the development branch, DESeq2 v1.3. This version will become
the release branch in ~1 month. We created a simple class 'DESeqResults' on
top of DataFrame, so that downstream packages can design methods specific
for DESeq2 results objects.

In the release branch (v1.2) you can produce an MA plot using the
DESeqDataSet object:

plotMA(dds)

FYI, you can always pull up the vignette appropriate for your version by
loading it from your R session:

vignette("DESeq2")

Mike


> I just don't understand how to make plotMA display the results.  Using the
> command syntax that you provide:
> plotMA(res,main="DESeq2",ylim=c(-2,2))
> I get this error:
> Error in plotMA(res, main = "DESeq2", ylim = c(-2, 2)) :
>   Error from the generic function 'plotMA' defined in package
> 'BiocGenerics': no S4 method definition for argument 'res' of class
> 'DataFrame' 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 have tried calling plotMA from limma as suggested, yielding:
> Error in as.vector(data) :
>   no method for coercing this S4 class to a vector

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