​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 [[alternative HTML version deleted]]

Mike, this is so helpful. Thanks much! David On Sun, 16 Mar 2014 17:19:12 -0400 Michael Love <michaelisaiahlove at="" gmail.com=""> wrote: >?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