[BioC] errors in using edgeR

[Wang, Li]

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