We recommend you use RStudio for this class, on all operating systems. You can use the following link http://www.rstudio.com/ide/download/ or good old fashioned google.
If you want to extract the R code only from a markdown file, use the following command in the library knitr called purl.
library(knitr)
knitr::purl("01_raw2dge.Rmd")
The affy vignette is a very good source, and is highly recommended. You can get this by installing and then just running vignette(“affy”) .
The very comprehensive tutorial section by UC-Riverside http://manuals.bioinformatics.ucr.edu/ .
R-Markdown is a very good tool to document your code, and figure out exactly where you are going wrong. The R Package knitr, does a fantastic job and is very well documented. All these class materials have been produced using knitr.
limma vignette which is available on Bioconductor. http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf
More information on how to make robust design matrices for experiments can be found in, Statistics for Biology and Health - Springer, Chapter V, Page 399-417.http://www.statsci.org/smyth/pubs/limma-biocbook-reprint.pdf