Installation instructions for JAX_RepAffyMaanovaAnalysis.pipeline

Installation:

  1. Have a GenePattern server (version 3.1) locally installed on your computer.
  2. On that computer, have the R/maanova package (version 1.8 or greater) from Bioconductor (http://bioconductor.org) installed along with the base Bioconductor and R/qvalue packages (see below for tips).
  3. Using the GenePattern web interface, log onto GenePattern.
  4. At the top of the GenePattern home page, click on the “Modules & Pipelines” pull down menu item and select the “Install from zip” item.
  5. In the resulting page, specify the location of the downloaded .zip using the “Browse…” button.  Next, select whether you want the pipeline accessible to the current user or all users on the system.  Finally, click the “Install” button.
  6. After the installation process is complete, you should see a new item under the pipeline menu on the left.  It should appear as “JAX_RepAffyMaanovaAnalysis.pipeline”.  In addition, two new modules will appear as “JAX_AffyProcessing” and “JAX_AffyMaanova” under the modules menu also on the left.

You will need a comma separated annotation file from Affymetrix® specific to the Affymetrix chip used in the experiment. For the Mouse Genome 430 2.0 Array, you would use this file. (You may need to register with Affymetrix to download.)

Tips--instructions for installing packages required for JAX_RepAffyMaanovaAnalysis.pipeline

To install Bioconductor version 2.0 packages that are compatible with R 2.5.1:

Start R version 2.5.1 (2007-06-27), and type:

source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite("qvalue")

For R/maanova 1.8.1 and R/maanova 1.10.0 that were released with Bioconductor version 2.1 or version 2.2, the follow these steps:

Windows:

Manually download installation files for windows to the local computer (R/maanova Version 1.8.1 can be obtained from here or here and R/maanova version 1.10.0 can be obtained from here).

Assuming the zip file is located under "C:/Program Files/R/R-2.5.1/"
In R version 2.5.1, type:

install.packages("C:/Program Files/R/R-2.5.1/maanova_1.8.1.zip", contriburl=NULL)

OR

install.packages("C:/Program Files/R/R-2.5.1/maanova_1.10.0.zip", contriburl=NULL)

Linux:

Download installation files for Linux.

Log in as root user, type:

R CMD INSTALL maanova_1.8.1.tar.gz

OR

R CMD INSTALL maanova_1.10.0.tar.gz

Mac

R 2.5.1 and maanova 1.8.1 and 1.10 are not compatible on the Mac.