### goldenspike R package: Unix Installation Instructions.

- Install the statistical programming language R. R Project Download. There are detailed R installation instructions here.
- Install Bioconductor. Note: within R, use the command
##### getBioC(libName="affy")

- Install the goldenspike R package.
- Download the goldenspike R package.
- At the shell command prompt, say:
##### R CMD INSTALL goldenspike_03.tar.gz

.

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

loads the goldenspike library.
##### 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.
##### 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.
##### 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.
##### do.unpaired.comparisons()

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