Use of autocorrelation scanning in DNA copy number analysis.

ABSTRACT:

Motivation

Data quality is a critical issue in the analyses of DNA copy number alterations obtained from microarrays. It is commonly assumed that copy number alteration data can be modeled as piecewise constant and the measurement errors of different probes are independent. However, these assumptions do not always hold in practice. In some published datasets, we find that measurement errors are highly correlated between probes that interrogate nearby genomic loci, and the piecewise-constant model does not fit the data well. The correlated errors cause problems in downstream analysis, leading to a large number of DNA segments falsely identified as having copy number gains and losses.

Method

We developed a simple tool, called autocorrelation scanning profile, to assess the dep

SUBMITTER: Zhang L 

PROVIDER: S-EPMC3799475 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature