MGH BASE Plug-ins

BASE is a free, web-based solution for storing, managing, and analyzing large amounts of microarray expression data. This open source (GPL) effort is spearheaded by developers at Lund University in Sweden. This system was described in Saal LH, Troein C, Vallon-Christersson J, Gruvberger S, Borg A, and Peterson C, BioArray Software Environment: a platform for comprehensive management and analysis of microarray data, Genome Biology 2002, 3(8):software0003.1-0003.6

Bioinformatics staff at MGH also contributed to the development of BASE through bug fixes, testing, and most notably, the data analysis plug-in module described below.

MGH Analysis Suite

Current version: 1.1.1

This package provides five new "applications" that can be run from BASE (unique plug-in IDs are given in parentheses):

1. Fold ratio calculator (molbio.mgh.harvard.edu/dpark/foldratio)
   Computes "fold ratio" per each reporter via mean/median/etc of spot intensity ratios. Can return fold ratios as a reporterlist. Can plot histogram of fold ratios.
2. p-value calculator (molbio.mgh.harvard.edu/dpark/pvalue)
   Computes p-values for reporters. Can return p-values as a reporterlist. Can plot histogram of p-values and produce volcano plots. Uses 1-group t-test or Wilcoxon signed rank test.
3. Average "A" value calculator (molbio.mgh.harvard.edu/dpark/avgA)
   Computes "A" (1/2*log10(Ch1*Ch2)) per each reporter via mean/median/etc of spot A values. Can return A values as a reporterlist. Can plot histogram of A's.
4. Average channel intensity (molbio.mgh.harvard.edu/dpark/avgint)
   Computes "average channel intensity" per each reporter for a specified channel via mean/median/etc. Can return values as a reporterlist. Can plot histogram of average intensity.
5. Intensity limiter (molbio.mgh.harvard.edu/dpark/limitint)
   Enforce a lower limit to spot intensity values, replacing them with the lower limit instead of filtering them out. Useful to retain low (or zero or negative) intensity spots w/o causing mathematical trouble.

Requirements

• A recent (1.2.9 or greater) version of BASE
• Perl
• R
• R-sma (Terry Speed's statistical microarray analysis package for R)
• ghostscript (only if you want to produce pictures with the plug-ins)

These plug-ins are known to work with Perl 5.6.1, ghoscript 7.05.3-57, R 1.6.2, and R-sma 0.5.10.R0. They might work with earlier versions. The intensity limiter plug-in only requires Perl and does not use R, R-sma, or ghostscript.

Software info

The plug-ins were written in Perl and R. All code was written in the Bioinformatics Group, Molecular Biology dept of the Massachussetts General Hospital, funded by the PGA. Because it has adopted the BASE plug-in devkit, which is GPL'ed, this package, by extension, is covered by the GPL.

Downloading

As of BASE version 1.2.10, this MGH plug-in suite has been incorporated in the standard distribution of BASE. If you have downloaded a recent version of BASE, you do not need to download the MGH plug-ins separately. Go to the contrib/molbio.mgh.harvard.edu-dpark/ directory in the BASE distribution and follow the installation instructions below.

If you are using BASE version 1.2.9, you can obtain the package here. Download and unpack it.

Installing

Installation is straightforward. Unpack the file and run the following commands from the molbio.mgh.harvard.edu-dpark directory (don't include $ signs):

$ ./bootstrap
$ ./configure --prefix=path/to/base

where path/to/base defaults to /usr/local/base if not specified. Give the same prefix you gave when installing BASE. For the next step, make sure BASE is running and you are root (or someone with appropriate permissions):

$ make install

If all goes well, the plug-ins will be installed somewhere in the plugins/bin directory of your BASE installation and the plug-in defintion files will be imported into the database. The one remaining thing to do before using them is to go in through the web interface and activate the plug-ins and share them with an appropriate set of users (for instance make it world-readable). If you are just upgrading from an older version of this suite, the owner/group and privileges will be unaltered.

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