The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies |
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| Authors: | Roel GW Verhaak Frank JT Staal Peter JM Valk Bob Lowenberg Marcel JT Reinders Dick de Ridder |
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| Affiliation: | (1) Department of Hematology, Erasmus Medical Center, Rotterdam, The Netherlands;(2) Department of Immunology, Erasmus Medical Center, Rotterdam, The Netherlands;(3) Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, the Netherlands |
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| Abstract: | Background Intensity values measured by Affymetrix microarrays have to be both normalized, to be able to compare different microarrays by removing non-biological variation, and summarized, generating the final probe set expression values. Various pre-processing techniques, such as dChip, GCRMA, RMA and MAS have been developed for this purpose. This study assesses the effect of applying different pre-processing methods on the results of analyses of large Affymetrix datasets. By focusing on practical applications of microarray-based research, this study provides insight into the relevance of pre-processing procedures to biology-oriented researchers. |
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