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Transcript mapping with high-density oligonucleotide tiling arrays

Bioconductor version: Release (3.1)

The package provides functionality that can be useful for the analysis of high-density tiling microarray data (such as from Affymetrix genechips) for measuring transcript abundance and architecture. The main functionalities of the package are: 1. the class 'segmentation' for representing partitionings of a linear series of data; 2. the function 'segment' for fitting piecewise constant models using a dynamic programming algorithm that is both fast and exact; 3. the function 'confint' for calculating confidence intervals using the strucchange package; 4. the function 'plotAlongChrom' for generating pretty plots; 5. the function 'normalizeByReference' for probe-sequence dependent response adjustment from a (set of) reference hybridizations.

Author: Wolfgang Huber, Zhenyu Xu, Joern Toedling with contributions from Matt Ritchie

Maintainer: Zhenyu Xu <zhenyu at>

Citation (from within R, enter citation("tilingArray")):


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PDF R Script Introduction to the plotAlongChrom function
PDF R Script Introduction to using the segment function to fit a piecewise constant curve
PDF R Script Normalisation with the normalizeByReference function in the tilingArray package
PDF R Script Segmentation demo
PDF R Script Supplement. Calculation of the cost matrix
PDF   Reference Manual


biocViews Microarray, OneChannel, Preprocessing, Software, Visualization
Version 1.46.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 10.5 years)
License Artistic-2.0
Depends R (>= 2.11.0), Biobase, methods, pixmap
Imports strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4
Depends On Me davidTiling
Imports Me ADaCGH2, snapCGH
Suggests Me
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