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To get the development version of Bioconductor you can go to Biocondcutor http://www.bioconductor.org/ and use the getBioC script

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Installing Bioconductor

Bioconductor is open source software used for microarray analysis.

http://gentleman.fhcrc.org/Ghent/UsingR

Notes to help select the right versions of the software.

It will be best if you use the development version of R and the development version of Bioconductor. For R that is version 2.1.0 (or more explicitly the 2.1.0 release candidate).

The reason that this is a good idea is that most of the packages have been improved quite substantially over the past three months, in preparation for the book, and we should make use of some of those improvements.

You can get the Windows development version of R from R Devel for Windows among many other places.

http://cran.univ-lyon1.fr/bin/windows/base/index.html rw2001.exe

For those of you using Linux I recommend either downloading the tarball available from CRAN or using the subversion archive.

To get the development version of Bioconductor you can go to Biocondcutor http://www.bioconductor.org/ and use the getBioC script. Be careful to use the

develOK=TRUE flag though. After that you can use install.packages2, again you should always set develOK=TRUE when using this.

I will make available, through the course web site, all packages for the upcoming Bioconductor Book. You will be able to download them and then run examples etc.

Install Bioconductor

1. From your R session, type:

source("http://www.bioconductor.org/getBioC.R")

this will download the getBioC functionality into your R session.

2. To install Bioconductor packages, use the function "getBioC" as follows. To download and install the default packages, type:

getBioC()

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Exercises

Open R session Load libraries Set path

Session 1: data visualization and preprocessing (marray.R) Session 2: SAM.R

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