Simone <enomis.bioc at="" ...=""> writes: > > Dear Simone, I have the same issue as yours, with different samples though. I am unable to plot plotDispEsts > plotDispEsts(mycIdaxVsdbmExons) Error: is(cds, "CountDataSet") is not TRUE Did you get a fix for this or are you using the older version? Ashu

Dear Ashu, well, the fix was what Wolfgang Huber wrote - running the code of the function contained in DEXSeq to have it in the workspace. This one works. I paste Wolfgang's reply here again: > Your problem with 'plotDispEsts' is an oversight of ours > in the last release of the DEXSeq package: the function > 'plotDispEsts' in the DEXSeq vignette is defined 'on the fly' > in the global workspace by the vignette (see > http://bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/ doc/DEXSeq.R > chunk 10). What happens in your case is that you probably > didn't run this, and picked up the DESeq::plotDispEsts function > instead, which throws the error. The sane solution, of course, > would be for us to define this as a generic function (e.g. in > BiocGenerics) and dispatch on argument type. This will be > the case in the next release. Till then, as a workaround, > please run the R code in the vignette from the .R file provided > with the package, rather than copy-pasting it from the PDF. In my case, this solved the problem. (But I am still struggling with the MA plot ...) Hope that helps. Best wishes, Simone On Fri, Jun 21, 2013 at 8:00 PM, Ashu <ashu.chawla07 at="" gmail.com=""> wrote: > Simone <enomis.bioc at="" ...=""> writes: > > >> >> > > > > Dear Simone, > > I have the same issue as yours, with different samples though. I am unable > to plot plotDispEsts > >> plotDispEsts(mycIdaxVsdbmExons) > Error: is(cds, "CountDataSet") is not TRUE > > Did you get a fix for this or are you using the older version? > > Ashu > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor