Re: errors in using edgeR

Dear Li,

Please follow the posting guide:

http://www.bioconductor.org/help/mailing-list/posting-guide/

and provide output from sessionInfo().  My guess is that you are reading 
the User's Guide for edgeR that is part of Bioconductor 2.10 released a 
few weeks ago, but actually using a much older version of R and edgeR.

The function cpm() for example was introduced with Bioconductor Release 
2.9 more than six months ago:

   http://www.bioconductor.org/news/bioc_2_9_release/

so the Bioconductor software you are using must be Release 2.8 or earlier.

Best wishes
Gordon

---------------------------------------------
Professor Gordon K Smyth,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
smyth@...
http://www.wehi.edu.au
http://www.statsci.org/smyth

On Fri, 13 Apr 2012, Wang, Li wrote:

> 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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