[BioC] experiment design in EdgeR -- correction
guest at bioconductor.org
Thu Oct 25 22:56:55 CEST 2012
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?
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,]
-- output of sessionInfo():
R version 2.15.1 (2012-06-22)
Platform: i386-pc-mingw32/i386 (32-bit)
 LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252
 LC_MONETARY=French_France.1252 LC_NUMERIC=C
attached base packages:
 stats graphics grDevices utils datasets methods base
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