experiment design in EdgeR -- correction
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Guest User ★ 13k
@guest-user-4897
Last seen 9.5 years ago
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, anna -- output of sessionInfo(): R version 2.15.1 (2012-06-22) Platform: i386-pc-mingw32/i386 (32-bit) locale: [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 -- Sent via the guest posting facility at bioconductor.org.
edgeR edgeR • 596 views
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