A comparison of match-only algorithms for the analysis of Plasmodium falciparum oligonucleotide arrays
- Author(s)
- Simpson, KM; Baum, J; Good, RT; Winzeler, EA; Cowman, AF; Speed, TP;
- Details
- Publication Year 2005-04-30,Volume 35,Issue #5,Page 523-531
- Journal Title
- INTERNATIONAL JOURNAL FOR PARASITOLOGY
- Publication Type
- Journal Article
- Abstract
- This study is motivated by two data sets which employ a custom Plasmodium falciparum version of the Affymetrix GeneChip (R), 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. (c) 2005 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.
- Publisher
- PERGAMON-ELSEVIER SCIENCE LTD
- Keywords
- PROBE LEVEL; MICROARRAY; NORMALIZATION; DISCOVERY; DESIGN
- Publisher's Version
- https://doi.org/10.1016/j.ijpara.2005.02.010
- Terms of Use/Rights Notice
- Refer to copyright notice on published article.
Creation Date: 2005-04-30 12:00:00