Software note: using probe secondary structure information to enhance Affymetrix GeneChip background estimates

Comput Biol Chem. 2007 Apr;31(2):92-8. doi: 10.1016/j.compbiolchem.2007.02.008. Epub 2007 Feb 20.

Abstract

High-density short oligonucleotide microarrays are a primary research tool for assessing global gene expression. Background noise on microarrays comprises a significant portion of the measured raw data. A number of statistical techniques have been developed to correct for this background noise. Here, we demonstrate that probe minimum folding energy and structure can be used to enhance a previously existing model for background noise correction. We estimate that probe secondary structure accounts for up to 3% of all variation on Affymetrix microarrays.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Gene Expression Profiling* / instrumentation
  • Gene Expression Profiling* / methods
  • Gene Expression Profiling* / statistics & numerical data
  • Models, Genetic*
  • Nucleic Acid Hybridization
  • Oligonucleotide Array Sequence Analysis* / instrumentation
  • Oligonucleotide Array Sequence Analysis* / methods
  • Oligonucleotide Array Sequence Analysis* / statistics & numerical data
  • Oligonucleotide Probes / chemistry*
  • Software*

Substances

  • Oligonucleotide Probes