[BioC] egdeR troubles under new R 3.02

[Gordon K Smyth]

> Date: Tue, 8 Oct 2013 22:42:33 -0400 (EDT)
> From: alogmail2 at aol.com
> To: bioconductor at r-project.org
> Subject: [BioC] egdeR troubles under new R 3.02
>
> Dear All,
>
> It seems edgeR has a bug under new R 3.0.2.

Poor edgeR!  None of the functions you use here even belong to the 
edgeR package.

Gordon

> 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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