Understanding the physics of oligonucleotide microarrays: the Affymetrix spike-in data reanalysed.
The Affymetrix U95 and U133 Latin-Square spike-in datasets are reanalysed, together with a dataset from a version of the U95 spike-in experiment without a complex non-specific background. The approach uses a physico-chemical model which includes the effects of the specific and non-specific hybridization and probe folding at the microarray surface, target folding and hybridization in the bulk RNA target solution and duplex dissociation during the post-hybridization washing phase. The model predicts a three-parameter hyperbolic response function that fits well with fluorescence intensity data from all the three datasets. The importance of the various hybridization and washing effects in determining each of the three parameters is examined, and some guidance is given as to how a practical algorithm for determining specific target concentrations might be developed.
Burden
Conrad J
CJ
Centre for Bioinformation Science, John Curtin School of Medical Research and Mathematical Sciences Institute, Australian National University, Canberra, ACT 0200, Australia. Conrad.Burden@anu.edu.au
D000465:Algorithms; D020137:Base Pair Mismatch / Q000235:genetics; D020029:Base Pairing / Q000235:genetics; D001703:Biophysics / Q000379:methods*; D002460:Cell Line; D015342:DNA Probes / Q000737:chemistry / Q000235:genetics; D006801:Humans; D008956:Models, Chemical; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012313:RNA / Q000737:chemistry / Q000235:genetics
D015342:DNA Probes; D012313:RNA