updated analysis.Rmd from @lis-is, fixed countdata issue with copy
minor edit
Merge pull request #1 from bioconnector/rnaseq-rmd

Merging this in. Still need to fix a few things @liz-is and @rbeagrie. HTML not compiling because trying to `install.packages(...)` without specifying a mirror. Perhaps best to include the package installation commands in a chunk with `eval=FALSE` so doesn't download package every time try to compile.
fixed conflicts