Comparison of sequence-dependent tiling array normalization approaches.

ABSTRACT:

Background

The detection of enriched DNA or RNA fragments by tiling microarrays has become more and more popular. These microarrays contain a high number of small probes covering genomic loci. However, to achieve high coverage the probe sequences cannot be selected for their hybridization properties. The affinity of the probes towards their targets varies in a sequence-dependent manner. In order to remove this bias a number of approaches have been developed and shown to increase the detection of enriched DNA or RNA fragments. However, these approaches also employ a peak detection algorithm that is different from the one used previously. Thus, it seems possible that the enhancement of detection is due to the peak detection algorithm rather than the sequence-dependent normalization.<

SUBMITTER: Chung HR 

PROVIDER: S-EPMC2753852 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature