Model-based analysis of two-color arrays (MA2C)

Genome Biol. 2007;8(8):R178. doi: 10.1186/gb-2007-8-8-r178.


A novel normalization method based on the GC content of probes is developed for two-color tiling arrays. The proposed method, together with robust estimates of the model parameters, is shown to perform superbly on published data sets. A robust algorithm for detecting peak regions is also formulated and shown to perform well compared to other approaches. The tools have been implemented as a stand-alone Java program called MA2C, which can display various plots of statistical analysis for quality control.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • Animals
  • Base Sequence
  • Caenorhabditis elegans / genetics
  • Carbocyanines / analysis
  • Computational Biology / methods*
  • Fluorescent Dyes / analysis*
  • Nucleic Acid Probes / chemistry*
  • Oligonucleotide Array Sequence Analysis / standards*
  • Software*


  • Carbocyanines
  • Fluorescent Dyes
  • Nucleic Acid Probes
  • cyanine dye 3
  • cyanine dye 5