CMARRT: a tool for the analysis of ChIP-chip data from tiling arrays by incorporating the correlation structure.

ABSTRACT: Whole genome tiling arrays at a user specified resolution are becoming a versatile tool in genomics. Chromatin immunoprecipitation on microarrays (ChIP-chip) is a powerful application of these arrays. Although there is an increasing number of methods for analyzing ChIP-chip data, perhaps the most simple and commonly used one, due to its computational efficiency, is testing with a moving average statistic. Current moving average methods assume exchangeability of the measurements within an array. They are not tailored to deal with the issues due to array designs such as overlapping probes that result in correlated measurements. We investigate the correlation structure of data from such arrays and propose an extension of the moving average testing via a robust and rapid method called CMARRT.

SUBMITTER: Kuan PF 

PROVIDER: S-EPMC2862456 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature