Supplementary Material
Scharpf RB, Ting JC, Pevsner J, Ruczinski I (2007).
SNPchip: R Classes and Methods for SNP Array Data
Bioinformatics, 23(5): 627-8.
Here is how to install everything you need:
- Install R (a free software environment for statistical computing and graphics) from CRAN. The FAQs and Manuals contain detailed instructions for installing R on various platforms.
- Install Bioconductor by following the Bioconductor How To Install guidelines. In particular, the following sets of commands, typed at the R prompt, should work:
> source("http://bioconductor.org/biocLite.R")
> biocLite()
- Check the version requirements and dependencies of the SNPscan from its Bioconductor page or the version change log, and install the required packages. Currently the geneplotter package is released, and the oligo package is developmental. So for now, type
> biocLite("geneplotter")
and install the oligo package using the source code from the Bioconductor oligo page (see below for more instructions on how to do that). Once the oligo package is released, the following line should do all in one wash-up:
> biocLite(c("geneplotter", "oligo"))
Note that the Biobase package has been installed as one of the default packages.
- Install the package:
Currently, SNPchip is not a released package. It is developmental, and available in the BioC2.0 repository. Go to the Bioconductor SNPchip page and download the source code or the Windows binary. For Unix/Linux, SNPchip can be installed by typing (at the Linux/Unix prompt, after unzipping/untarring)
$ R CMD INSTALL SNPchip
For Windows, double-click on the binary.