Journal
FRONTIERS IN BIOSCIENCE-LANDMARK
Volume 13, Issue -, Pages 2714-2720Publisher
FRONTIERS IN BIOSCIENCE INC
DOI: 10.2741/2878
Keywords
dimension reduction; principal component analysis; mixed effects model; microarray
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Funding
- NATIONAL CANCER INSTITUTE [R03CA114688] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF DENTAL &CRANIOFACIAL RESEARCH [K22DE014847, R03DE016569] Funding Source: NIH RePORTER
- NCI NIH HHS [CA114688] Funding Source: Medline
- NIDCR NIH HHS [DE016569, DE014847] Funding Source: Medline
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The rapid advances in high-throughput microarray technologies greatly facilitate the disease biomarker discovery. However, the potential of these microarray data has not yet been fully utilized. This is partly due to the limited sample sizes of each individual study. Combining microarray data from multiple studies improves the statistical power of detecting differentially expressed genes. Here we present a method for combining the microarray datasets at array probeset level. Using datasets from two commonly used array platforms, the Affymetrix Human Genome U133A and Human Genome U133 Plus 2.0 arrays, we found laboratory effects may be more influential than the platform effect. A visualization scheme for merging the array data from different array platforms was proposed to qualitatively judge the degree of agreement between datasets. A mixed-effects model was applied to identify differentially expressed genes from the merged array data.
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