The package implements a method for normalising microarray intensities, and works for single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have similar format. The method uses a robust variant of the maximum-likelihood estimator for an additive-multiplicative error model and affine calibration. The model incorporates data calibration step (a.k.a. normalization), a model for the dependence of the variance on the mean intensity and a variance stabilizing data transformation. Differences between transformed intensities are analogous to "normalized log-ratios". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.
Package details |
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Author | Wolfgang Huber, with contributions from Anja von Heydebreck. Many comments and suggestions by users are acknowledged, among them Dennis Kostka, David Kreil, Hans-Ulrich Klein, Robert Gentleman, Deepayan Sarkar and Gordon Smyth |
Bioconductor views | Microarray OneChannel Preprocessing TwoChannel |
Maintainer | Wolfgang Huber <wolfgang.huber@embl.de> |
License | Artistic-2.0 |
Version | 3.58.0 |
URL | http://www.r-project.org http://www.ebi.ac.uk/huber |
Package repository | View on Bioconductor |
Installation |
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