goldenspike R package: Unix Installation Instructions.

1. Install the statistical programming language R. R Project Download. There are detailed R installation instructions here.
2. Install Bioconductor. Note: within R, use the command

   getBioC(libName="affy")

3. Install the goldenspike R package.
   1. Download the goldenspike R package.
   2. At the shell command prompt, say:

      R CMD INSTALL goldenspike_03.tar.gz

      .
4. A brief description of R commands using this library:
   1. Go to a directory containing the Affymetrix CEL files for which you would like to calculate differential expression, and start R.

   2. library(goldenspike)

      loads the goldenspike library.

   3. help(package=goldenspike)

      lists all the functions within this library. Among these, three functions (mentioned below) can be used to perform the basic task of finding differentially expressed genes.

   4. make.expr.summaries()

      loads the CEL files within the directory and calculates 16 sets of expression summaries, which are saved in the files "[1-8].dat" and "[1-8]a.dat" within the current working directory.

   5. do.paired.comparisons()

      calculates differential expression statistics for a paired experimental design. This function will ask you which samples correspond to experiment/control, and request filenames which it will use to deposit output.

   6. do.unpaired.comparisons()

      calculates statistics for differential expression statistics for an unpaired experimental design.