[BioC] egdeR troubles under new R 3.02

[James W. MacDonald]

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.

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
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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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