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 ..