aroma-package: Package aroma

In HenrikBengtsson/aroma: An R Object-oriented Microarray Analysis package

Description

Methods for microarray analysis after the images have been scanned. Formerly known as the com.braju.sma package.

This package was formerly known as the com.braju.sma package. On 2003-12-31 it was renamed to the current name aroma, which is an achronym for An R Object-oriented Microarray Analysis package.

Requirements

This package depends on several other packages, namely R.methodsS3, R.oo, R.utils, aroma.light, R.basic, R.graphics, and R.io.

Installation

To install this package and all required package, see instructions at http://www.braju.com/R/.

To get started

To get started, see:

1. GenePixData, QuantArrayData, ScanAlyzeData, SpotData, or SpotfinderData.

2. For an overview of normalization and calibration methods, please see the aroma.light package.

3. calibrateMultiscan.RGData().

4. normalizeAffine.RGData().

Further readings

For an overview of aroma, see [1]. See also the online webpage of aroma - http://www.maths.lth.se/help/R/aroma/. Several of the normalization methods proposed in [3]-[5] are available in this package.

How to cite this package

Whenever using this package, please cite [1] as

@TECHREPORT{BengtssonH_2004,
  author = {Bengtsson, Henrik},
  title = {{aroma} - {A}n {R} {O}bject-oriented {M}icroarray
           {A}nalysis environment},
  institution = {Mathematical Statistics, Centre for Mathematical
                 Sciences, Lund University, Sweden},
  year = {2004},
  type = {{Preprint in Mathematical Sciences}},
  number = {2004:18},
}

@ARTICLE{BengtssonHossjer_2006,
  author = {Henrik Bengtsson and Ola H{\"o}ssjer},
  title = {Methodological study of affine transformations of gene
           expressiondata with proposed robust non-parametric
           multi-dimensional normalization	method},
  journal = {BMC Bioinformatics},
  year = {2006},
  volume = {7},
  number = {100},
  month = {mar},
  doi = {10.1186/1471-2105-7-100}
}

@ARTICLE{BengtssonH_etal_2004,
  author = {Henrik Bengtsson and G\"{o}ran J\"{o}nsson and
            Johan Vallon-Christersson},
  title = {Calibration and assessment of channel-specific biases
           in microarray data with extended dynamical range},
  journal = {BMC Bioinformatics},
  year = {2004},
  volume = {5},
  number = {177},
  doi = {10.1186/1471-2105-5-177},
}

Author(s)

Henrik Bengtsson (http://www.braju.com/R/)

References

Some of the reference below can be found at http://www.maths.lth.se/bioinformatics/publications/.

[1] H. Bengtsson, aroma - An R Object-oriented Microarray Analysis environment, Preprints in Mathematical Sciences (manuscript in preparation), Mathematical Statistics, Centre for Mathematical Sciences, Lund University, 2004.

[2] H. Bengtsson, The R.oo package - Object-Oriented Programming with References Using Standard R Code, In Kurt Hornik, Friedrich Leisch and Achim Zeileis, editors, Proceedings of the 3rd International Workshop on Distributed Statistical Computing (DSC 2003), March 20-22, Vienna, Austria. http://www.ci.tuwien.ac.at/Conferences/DSC-2003/Proceedings/

[3] Henrik Bengtsson and Ola Hössjer, Methodological Study of Affine Transformations of Gene Expression Data, Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dimensional normalization method, BMC Bioinformatics, 2006, 7:100.

[4] H. Bengtsson, J. Vallon-Christersson and G. Jönsson, Calibration and assessment of channel-specific biases in microarray data with extended dynamical range, BMC Bioinformatics, 5:177, 2004.

[5] H. Bengtsson, Identification and normalization of plate effects in cDNA microarray data, Preprints in Mathematical Sciences, 2002:28, Mathematical Statistics, Centre for Mathematical Sciences, Lund University, 2002.

HenrikBengtsson/aroma documentation built on May 7, 2019, 12:56 a.m.