tilingArray

Analysis of high-density oligonucleotide tiling arrays

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

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