title: Software note: using probe secondary structure information to enhance Affymetrix GeneChip background estimates.
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.
authors: Bioinformatics Research Center, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA.
authors: Raad Z
authors: RZ
authors: Gharaibeh
authors: Anthony A
authors: AA
authors: Fodor
authors: Cynthia J
authors: CJ
authors: Gibas
mesh_terms: D020869:Gene Expression Profiling / Q000295:instrumentation / Q000379:methods / Q000706:statistics & numerical data; D008957:Models, Genetic; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods / Q000706:statistics & numerical data; D015345:Oligonucleotide Probes / Q000737:chemistry*; D012984:Software
chemical_list: D015345:Oligonucleotide Probes