Software note: using probe secondary structure information to enhance Affymetrix GeneChip background estimates.
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.
Gharaibeh
Raad Z
RZ
Bioinformatics Research Center, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte, NC 28223, USA.
Fodor
Anthony A
AA
Gibas
Cynthia J
CJ
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
D015345:Oligonucleotide Probes