[BioC] plotMeanVar and coxreid method in edgeR

[Davis, Wade]

Dear Mark and Gordon:

I have a few questions and suggestions for the plotMeanVar function (which I think is very handy) in edgeR.
 
I receive the following message when trying to use dispersion.method="coxreid" in plotMeanVar: 

plotMeanVar(dge.ctl.filt, meanvar=ctl.filt.meanvar, show.tagwise.vars=TRUE, NBline=TRUE, dispersion.method="coxreid")
Error in plotMeanVar(dge.ctl.filt, meanvar = ctl.filt.meanvar, show.tagwise.vars = TRUE,  : 
  Could not extract Cox-Reid common dispersion. Try running CRDisp on the DGEList object before plotMeanVar.

I had run estimateGLMCommonDisp/estimateGLMTrendedDisp/estimateGLMTagwiseDisp  prior to this call, knowing that they have superseded CRDisp / estimateCRDisp / etc.

names(dge.ctl.filt)
[1] "samples"            "counts"             "all.zeros"          "common.dispersion"  "trended.dispersion" "abundance"         
[7] "bin.dispersion"     "bin.abundance"      "tagwise.dispersion"


NOTE: Everything runs without complaint with:
plotMeanVar(dge.ctl.filt, meanvar=ctl.filt.meanvar, show.tagwise.vars=TRUE, NBline=TRUE, dispersion.method="qcml")


Looking into the plotMeanVar source, it seems that the function is looking for elements object$CR.common.dispersion or object$CR.tagwise.dispersion. 


Snippet from plotMeanVar:
-------------------------------------------
   if (NBline | show.tagwise.vars) {
        if (dispersion.method == "coxreid") {
            common.dispersion <- object$CR.common.dispersion
            tagwise.dispersion <- object$CR.tagwise.dispersion
        }
        else {
            common.dispersion <- object$common.dispersion
            tagwise.dispersion <- object$tagwise.dispersion
        }
        if (is.null(common.dispersion)) {
            if (dispersion.method == "coxreid") 
                stop("Could not extract Cox-Reid common dispersion. Try running CRDisp on the DGEList object before plotMeanVar.\n")
            else stop("Could not extract qCML common dispersion. Try running estimateCommonDisp on the DGEList object before plotMeanVar.\n")
        }
    }
-------------------------------------------

It is my understanding that the names CR.* are not being used anymore for DGEList objects. I personally like the CR.* convention because as it stands now, I can't examine an DGEList object and tell by what dispersion method object$common.dispersion or estimateTagwiseDisp was obtained (i.e., estimateCommonDisp or estimateGLMCommonDisp).

So would you politely consider modifying the DGEList-class to address this? Or I have I misdiagnosed the problem entirely? 

Thanks for your insight on the matter and your time. 

My session info is below.
Wade


> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] limma_3.10.0 edgeR_2.4.1