In microarray analysis, people are interested in those features that have different characters in diseased samples compared to normal samples. The usual p-value method of selecting significant genes either gives too many false positives or cannot detect all the significant features. The False Discovery Rate (FDR) method controls false positives and at the same time selects significant features. We introduced Benjamini's method and Storey's method to control FDR, applied the two methods to human Meningioma data. We found that Benjamini's method is more conservative and that, after the number of the tests exceeds a threshold, increase in number of tests will lead to decrease in number of significant genes. In the second chapter, we investigate ways to search interesting gene expressions that cannot be detected by linear models as t-test or ANOVA. We propose a novel approach to use quadratic logistic regression to detect genes in Meningioma data that have non-linear relationship within phenotypes. By using quadratic logistic regression, we can find genes whose expression correlates to their phenotypes both linearly and quadratically. Whether these genes have clinical significant is a very interesting question, since these genes most likely be neglected by traditional linear approach.
Worcester Polytechnic Institute
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Guo, Ruijuan, "Sample comparisons using microarrays: - Application of False Discovery Rate and quadratic logistic regression" (2008). Masters Theses (All Theses, All Years). 28.
FDR, Logistic regression, Microarry, DNA microarrays, Logistic regression analysis