[BioC] DEXSeq: Problems trying to reproduce the example of the vignette

Simone enomis.bioc at gmail.com
Mon Jun 24 10:19:37 CEST 2013

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,

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
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