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