Description Requirements Installation To get started Further readings How to cite this package Author(s) References
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 20031231 it was renamed to the current name aroma, which is an achronym for An R Objectoriented Microarray Analysis package.
This package depends on several other packages, namely R.methodsS3, R.oo, R.utils, aroma.light, R.basic, R.graphics, and R.io.
To install this package and all required package, see instructions at
http://www.braju.com/R/.
To get started, see:
GenePixData
, QuantArrayData
, ScanAlyzeData
,
SpotData
, or SpotfinderData
.
For an overview of normalization and calibration methods,
please see the aroma.light
package.
calibrateMultiscan.RGData
().
normalizeAffine.RGData
().
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.
Whenever using this package, please cite [1] as
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35  @TECHREPORT{BengtssonH_2004,
author = {Bengtsson, Henrik},
title = {{aroma}  {A}n {R} {O}bjectoriented {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 nonparametric
multidimensional normalization method},
journal = {BMC Bioinformatics},
year = {2006},
volume = {7},
number = {100},
month = {mar},
doi = {10.1186/147121057100}
}
@ARTICLE{BengtssonH_etal_2004,
author = {Henrik Bengtsson and G\"{o}ran J\"{o}nsson and
Johan VallonChristersson},
title = {Calibration and assessment of channelspecific biases
in microarray data with extended dynamical range},
journal = {BMC Bioinformatics},
year = {2004},
volume = {5},
number = {177},
doi = {10.1186/147121055177},
}

Henrik Bengtsson (http://www.braju.com/R/)
Some of the reference below can be found at
http://www.maths.lth.se/bioinformatics/publications/.
[1] H. Bengtsson, aroma  An R Objectoriented 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  ObjectOriented 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 2022, Vienna, Austria. http://www.ci.tuwien.ac.at/Conferences/DSC2003/Proceedings/
[3] Henrik Bengtsson and Ola HÃ¶ssjer, Methodological Study of Affine Transformations of Gene Expression Data, Methodological study of affine transformations of gene expression data with proposed robust nonparametric multidimensional normalization method, BMC Bioinformatics, 2006, 7:100.
[4] H. Bengtsson, J. VallonChristersson and G. JÃ¶nsson, Calibration and assessment of channelspecific 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.
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