Physical Sciences and Mathematics Commons^™

Probe Level Analysis Of Affymetrix Microarray Data, Richard Ellis Kennedy

Theses and Dissertations

The analysis of Affymetrix GeneChip® data is a complex, multistep process. Most often, methodscondense the multiple probe level intensities into single probeset level measures (such as RobustMulti-chip Average (RMA), dChip and Microarray Suite version 5.0 (MAS5)), which are thenfollowed by application of statistical tests to determine which genes are differentially expressed. An alternative approach is a probe-level analysis, which tests for differential expression directly using the probe-level data. Probe-level models offer the potential advantage of more accurately capturing sources of variation in microarray experiments. However, this has not been thoroughly investigated, since current research efforts have largely focused on the …