[BioC] experiment design in EdgeR -- correction

anna [guest] guest at bioconductor.org
Thu Oct 25 22:56:55 CEST 2012

Dear Gordon,
before the last revision of the user's guide appears in the official release of edgeR,
I just would like to make a correction : new page 31 it is 18 RNA samples and not 9 RNA samples ( there are 9 patients, and 18 RNA libraries, treatment was done before RNA extraction).

second thing: for the new section, I guess dispersion calculations are the same? 

third thing:
section 4.4.4: this codes selects me the lowest transcript instead of highest,and adding decreasing=FALSE (or TRUE) did not help:
> o <- order(rowSums(y$counts))
> y <- y[o,]
> d <- duplicated(y$genes$Gene)
> y <- y[!d,]

Best regards,

 -- output of sessionInfo(): 

R version 2.15.1 (2012-06-22)
Platform: i386-pc-mingw32/i386 (32-bit)

[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252   
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C                  
[5] LC_TIME=French_France.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

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