[BioC] egdeR troubles under new R 3.02

[Wolfgang Huber]

On 9 Oct 2013, at 17:04, James W. MacDonald <jmacdon at uw.edu> wrote:
> On Wednesday, October 09, 2013 10:59:24 AM, Wolfgang Huber wrote:
>> On 9 Oct 2013, at 16:55, "James W. MacDonald" <jmacdon at uw.edu> wrote:
>>> 
>>> This is the sort of error you get when you have function masking. You loaded the limma package, which has a plotMA function, then you loaded (in an unknown order) the DESeq package, which also has a plotMA function, then you loaded DESeq2 which _also_ has a plotMA function.
>>> 
>> 
>> In Bioc 2.13, plotMA is a generic function in BiocGenerics and various other packages define their methods for that.
> 
> And that might actually matter if limma used S4 methods. But it does not, so the existence of a generic in this instance is irrelevant.

This design decision is up to the package maintainer, but the effort of wrapping a "normal" function into a method that is also registered with BiocGenerics::plotMA would be quite minimal (and not preclude being able to still call the normal function directly, as always.)

The concept of a project-wide common name space is probably elusive and ultimately misguided, but some approximation for the most popular name choices is what BiocGenerics attempts.

	Kind regards
	Wolfgang


> Best,
> 
> Jim
> 
> 
>> 
>> 	Best wishes
>> 	Wolfgang
>> 
>>> So when you say plotMA(<MArrayLM object>), R looks down the search path and sees the plotMA function in either DESeq or DESeq2 (whichever was loaded last), looks at the methods available, and says 'this function doesn't work on that sort of object'.
>>> 
>>> The work-around is to use limma::plotMA(), which tells R to look for the function in the correct package namespace.
>>> 
>>> Best,
>>> 
>>> Jim
>>> 
>>> 
>>>>> abline(h=0,col="darkgrey")
>>>> Error in int_abline(a = a, b = b, h = h, v = v, untf = untf, ...) :
>>>>   plot.new has not been called yet
>>>>> 
>>>> 
>>>> 
>>>> Thanks
>>>> 
>>>> 
>>>> Alex
>>>> 
>>>> 
>>>> UC Berkeley, Molecular Toxicology
>>>> Berkeley CA 94720
>>>> 
>>>> 
>>>> 
>>>> 
>>>>> sessionInfo()
>>>> R version 3.0.2 (2013-09-25)
>>>> Platform: i386-w64-mingw32/i386 (32-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] parallel  stats     graphics  grDevices utils     datasets  methods   base
>>>> 
>>>> 
>>>> other attached packages:
>>>>  [1] tweeDEseqCountData_1.0.9 DESeq2_1.1.45            RcppArmadillo_0.3.920.1  Rcpp_0.10.5              GenomicRanges_1.13.51    XVector_0.1.4
>>>>  [7] IRanges_1.19.38          DESeq_1.13.3             lattice_0.20-23          locfit_1.5-9.1           Biobase_2.21.7           BiocGenerics_0.7.5
>>>> [13] edgeR_3.3.8              limma_3.17.26            BiocInstaller_1.11.4
>>>> 
>>>> 
>>>> loaded via a namespace (and not attached):
>>>>  [1] annotate_1.39.0       AnnotationDbi_1.23.27 DBI_0.2-7             genefilter_1.43.0     geneplotter_1.39.05   grid_3.0.2
>>>>  [7] RColorBrewer_1.0-5    RSQLite_0.11.4        splines_3.0.2         stats4_3.0.2          survival_2.37-4       tools_3.0.2
>>>> [13] XML_3.98-1.1          xtable_1.7-1
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 	[[alternative HTML version deleted]]
>>>> 
>>>> 
>>>> 
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>>> 
>>> --
>>> James W. MacDonald, M.S.
>>> Biostatistician
>>> University of Washington
>>> Environmental and Occupational Health Sciences
>>> 4225 Roosevelt Way NE, # 100
>>> Seattle WA 98105-6099
>>> 
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
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>> 
> 
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099