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,
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):
- 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.
- 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.
- 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.
- 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.
- 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
- A recent (1.2.9 or greater) version of BASE
- 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,
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.
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
directory in the BASE distribution and follow the installation instructions
If you are using BASE version 1.2.9, you can obtain the package
and unpack it.
Installation is straightforward. Unpack the file and run the following
commands from the molbio.mgh.harvard.edu-dpark directory
(don't include $ signs):
$ ./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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