[BioC] egdeR troubles under new R 3.02

[Wolfgang Huber]

Dear Alex

this is because you have multiple packages in your search path that define a function "plotMA". Use the fully qualified path "limma::plotMA" to avoid the problem; alternatively, don't attach these other packages. This used to be DESeq in the last release, and it will be BiocGenerics in the next. (The latter now offers package authors the opportunity to register "plotMA" methods to that generic function, with their signature of choice, and spare users the confusion.) 

	Kind regards
	Wolfgang



On 9 Oct 2013, at 04:42, alogmail2 at aol.com wrote:

> Dear All,
> 
> 
> It seems edgeR has a bug under new R 3.0.2.
> 
> 
> Here is the example from LIMMA's guide for R-seq (p.111- etc):
> 
> 
> 
> library(tweeDEseqCountData)
>> data(pickrell1)
>> Counts <- exprs(pickrell1.eset)
>> class(Counts)
> [1] "matrix"
>> dim(Counts)
> [1] 38415    69
>> Counts[1:5,1:5]
>                NA18486 NA18498 NA18499 NA18501 NA18502
> ENSG00000127720       6      32      14      35      14
> ENSG00000242018      20      21      24      22      16
> ENSG00000224440       0       0       0       0       0
> ENSG00000214453       0       0       0       0       0
> ENSG00000237787       0       0       1       0       0
>> barplot(colSums(Counts)*1e-6, names=1:69, ylab="Library size (millions)")
>> Gender <- pickrell1.eset$gender
> 
> 
> 
> etc.
> 
> 
> It finally results in:
> 
> 
> 
> fit$df.prior
> [1] 4.6
>> summary(decideTests(fit))
>   (Intercept) Gendermale
> -1         292         43
> 0          913      17251
> 1        16105         16
>> chrom <- fit$genes$Chr
>> plotMA(fit,array=2,status=chrom,values=c("X","Y"),col=c("red","blue"),main="Male vs Female",legend="bottomright")
> Error in (function (classes, fdef, mtable)  : 
>  unable to find an inherited method for function ‘plotMA’ for signature ‘"MArrayLM"’
>> 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       
> 
> 
> 
> 
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> 
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