Permalink
Fetching contributors…
Cannot retrieve contributors at this time
93 lines (72 sloc) 3.1 KB
# Package aroma (2001-): Preprocessing of spotted microarray data
## aroma - Preprocessing of spotted microarray data
Developed since: 2001-03-10
Previously known as: com.braju.sma
Author: Henrik Bengtsson
Page last updated: 2011-02-26
Last successful installation: 2013-02-07
### Description
The aroma ("An R Object-oriented Microarray Analysis package") package
was first developed in March 2001 as an extension to the
<% cran('sma') %> ("Statistical Microarray Analysis") package
(Yee Hwa Yang et al.).
<% alert_warn({ %>
<strong>NOTE</strong>:
Despite its name, this package is independent of the other
packages in the Aroma Project framework. This page was added to the
Aroma Project website for the convenience of the users and developers
who are using this package.
<% }) %>
<% alert_warn({ %>
<strong>NOTE</strong>:
The development of this package has stopped. It is only kept to
a minimum such that it still installs. For two-color microarray
analysis, I recommend to use the <a href="http://www.bioconductor.org/packages/release/bioc/html/limma.html">limma</a> package available on Bioconductor.
<% }) %>
### Installation
In order to install the aroma package and all its dependencies
(including the sma package), in a fresh R session do:
```r
source("http://aroma-project.org/hbLite.R")
hbInstall("aroma")
```
You may see some warnings, especially while installing the sma package,
but you should *not* see/get any errors.
COMMENT: The sma package has been deprecated by its maintainer(s) and is
(as of Feb 2011) only available via the [CRAN
archives](http://cran.r-project.org/src/contrib/Archive/sma/). The last
available version (sma v0.5.15) will no longer install on recent R
version. For this reason, we have "patched" sma to v0.5.16 (not on
CRAN; only on the servers of the Aroma Project) by doing minimal fixes
such that it installs.
### Usage
After installation, load the aroma and the sma packages by:
```r
> library("aroma")
Loading required package: R.methodsS3
R.methodsS3 v1.4.2 (2012-06-22) successfully loaded. See ?R.methodsS3 for help.
Loading required package: R.oo
R.oo v1.11.7 (2013-01-08) successfully loaded. See ?R.oo for help.
Loading required package: R.utils
R.utils v1.19.5 (2013-01-11) successfully loaded. See ?R.utils for help.
Loading required package: aroma.light
Loading required package: matrixStats
matrixStats v0.7.0 (2013-01-14) successfully loaded. See ?matrixStats for help.
aroma.light v1.28.0 (2012-10-01) successfully loaded. See ?aroma.light for help.
Loading required package: R.graphics
Loading required package: R.basic
R.basic v0.52.0 (2013-02-07) successfully loaded. See ?R.basic for help.
Loading required package: R.colors
R.colors v0.6.0 (2013-02-07) successfully loaded. See ?R.colors for help.
R.graphics v0.44.0 (2013-02-07) successfully loaded. See ?R.graphics for help.
aroma v0.97.0 (2013-02-07) successfully loaded. See ?aroma for help.
> library("sma")
>
```
To further assert that the packages were successfully installed, try one
of the examples, e.g.
```r
> example(GenePixData)
```
This should load some example data and generate a log-ratio
log-intensity scatter plot.