[BioC] errors in using edgeR
Wang, Li
li.wang at ttu.edu
Sat Apr 14 00:41:30 CEST 2012
Dear Gordon and list
I am trying to do some analyses similar to the last case study in the user guide of edgeR and confronted with some errors:
1. keep <- rowSums(cpm(x)>0) >= 4
Error in inherits(x, "data.frame") : could not find function "cpm"
2. > els <- y$samples$lib.size * y$samples$norm.factors
> aug.count <- 2*ncol(bals)*els/sum(els)
> logCPM <- log2( (t(bals)+aug.count))
> plotMDS(logCPM, main="logFC BCV distance")
Error in sort.int((x[, i] - x[, j])^2, partial = topindex) :
index -495 outside bounds
3.> design <- model.matrix(~group)
> logFC <- predFC(y,design)
Error: could not find function "predFC"
4. > y <- estimateGLMTrendedDisp(y, design)
Loading required package: splines
> y <- estimateGLMTagwiseDisp(y, design)
> plotBCV(y)
Error: could not find function "plotBCV"
5. > cpm(y)[top,order(y$samples$group)]
Error: could not find function "cpm"
Most of them are about "could not find function ***". The related packages (edgeR, limma and qvalue) are all installed and loaded.
So, I am very curious to know why it cannot find functions.
I will appreciate your reply very much!
Best wishes
Li
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