COCAS

COCAS performs normalization and analysis of Chromatin immunoprecipitation microarray (ChIP-on-chip) data, optimized for Agilent microarrays scanned with an Agilent scanner, to correct unknown proportionality constants between measured intensities and mRNA copy numbers and enable accurate cross-array comparisons.

Key Features:

• Normalization Methodology: Addresses the unknown constant of proportionality between measured intensities and the number of mRNA copies per cell to improve comparisons across arrays.
• Centralization Technique: Implements a biologically motivated two-step centralization normalization to provide robust and consistent scaling across samples.
• Pairwise Quotient Estimation: Estimates the quotient of proportionality constants for each pair of arrays as the first step of centralization.
• Optimal Scaling Computation: Computes an optimally consistent scaling from the matrix of pairwise quotients to derive uniform normalization factors.

Scientific Applications:

• Genomic research: Supports ChIP-on-chip experiments requiring precise quantification and comparison of chromatin interactions.
• Gene regulation studies: Enables comparison of binding or enrichment profiles relevant to analyses of transcriptional regulation.
• Epigenetic and chromatin modification analysis: Facilitates investigations of epigenetic modifications and chromatin state mapping using Agilent ChIP-on-chip data.

Methodology:

Centralization two-step normalization consisting of pairwise estimation of quotients between array proportionality constants followed by computation of an optimally consistent scaling from the pairwise-quotient matrix.