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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