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This is the development version of tilingArray; for the stable release version, see tilingArray.

Transcript mapping with high-density oligonucleotide tiling arrays

Bioconductor version: Development (3.3)

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 <zxu at>

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


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


biocViews Microarray, OneChannel, Preprocessing, Software, Visualization
Version 1.49.0
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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