tilingArray

tilingArray analyzes high-density DNA tiling microarray data from platforms such as Affymetrix GeneChips to segment hybridization signals, infer transcript boundaries, and apply probe-specific background correction and scaling for measuring transcript abundance and transcript architecture in eukaryotic genomes.

Key Features:

• Segmentation of Hybridization Signal: Segments hybridization intensities along genomic coordinates to identify transcript boundaries from tiling microarray probes.
• Quantitative Comparability Adjustment: Uses a dynamic programming algorithm to compute a globally optimal piecewise-constant expression profile that enables quantitative comparison across probes despite sequence-dependent response differences.
• Probe-Specific Background Correction and Scaling: Performs probe-specific background correction and scaling using empirical probe response parameters derived from reference hybridizations, eliminating the need for paired mismatch probes.

Scientific Applications:

• Complete Transcriptome Characterization: Characterizes complete transcriptomes using high-density DNA tiling microarrays to accurately map transcript boundaries in eukaryotic genomes.
• Transcription Architecture and Dynamics: Supports analysis of transcriptional architecture and dynamical changes by providing adjusted, comparable probe-level expression profiles.

Methodology:

Dynamic programming to fit a globally optimal piecewise-constant expression profile, segmentation of hybridization signal along genomic coordinates, and probe-specific background correction and scaling using empirical probe response parameters from reference hybridizations.