title: A comparison of match-only algorithms for the analysis of Plasmodium falciparum oligonucleotide arrays.
abstract: This study is motivated by two data sets which employ a custom Plasmodium falciparum version of the Affymetrix GeneChip, containing only perfect match (PM) oligonucleotides. A PM-only chip cannot be analysed using the standard Affymetrix-supplied software. We compared the performance of three match-only algorithms on these data: the Match Only Integral Distribution (MOID) algorithm, Robust Multichip Analysis (RMA), and the Model Based Expression Index (MBEI). We validated the differential expression of several genes using quantitative reverse transcriptase-PCR. We also performed a comparison using two publicly available 'benchmarking' data sets: the Latin Square spike-in data set generated by Affymetrix, and the Gene Logic dilution series. Since we know what the true fold changes are in these special data sets, they are helpful for assessment of expression algorithms.
authors.affiliation: The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Vic. 3050, Australia. ksimpson@wehi.edu.au
authors.forename: K M
authors.initials: KM
authors.lastname: Simpson
authors.forename: J
authors.initials: J
authors.lastname: Baum
authors.forename: R T
authors.initials: RT
authors.lastname: Good
authors.forename: E A
authors.initials: EA
authors.lastname: Winzeler
authors.forename: A F
authors.initials: AF
authors.lastname: Cowman
authors.forename: T P
authors.initials: TP
authors.lastname: Speed
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology; D020869:Gene Expression Profiling; D017125:Genes, Protozoan; D020411:Oligonucleotide Array Sequence Analysis; D010963:Plasmodium falciparum / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA