There are several new versions of BioConductor edger available upstream. Unfortunanetly this needs r-cran-locfit which is non-free and not packaged (basically due to the lack of motivation to package non-free stuff) see http://bugs.debian.org/731599 The file inst/doc/edgeRUsersGuide.pdf has been removed from the original upstream package, as it was not accompanied by its source. It can be downloaded at the following URL. http://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf