It is common to test many hypotheses simultaneously in the application of statistics. The probability of making a false discovery grows with the number of statistical tests performed. When all the null hypotheses are true, and the test statistics are indepen- dent and continuous, the error rates from the family wise error rate (FWER)- and the false discovery rate (FDR)-controlling procedures are equal to the nominal level. When some of the null hypotheses are not true, both procedures are conservative. In the first part of this study, we review the background of the problem and propose methods to estimate the number of true null hypotheses. The estimates can be used in FWER- and FDR-controlling procedures with a consequent increase in power. We conduct simulation studies and apply the estimation methods to data sets with bio- logical or clinical significance. In the second part of the study, we propose a mixture model approach for the analysis of ChIP-chip high density oligonucleotide array data to study the interac- tions between proteins and DNA. If we could identify the specific locations where proteins interact with DNA, we could increase our understanding of many important cellular events. Most experiments to date are performed in culture on cell lines, bac- teria, or yeast, and future experiments will include those in developing tissues, organs, or cancer biopsies, and they are critical in understanding the function of genes and proteins. Here we investigate the ChIP-chip data structure and use a beta-mixture model to help identify the binding sites. To determine the appropriate number of components in the mixture model, we suggest the Anderson-Darling testing. Our study indicates that it is a reasonable means of choosing the number of components in a beta-mixture model. The mixture model procedure has broad applications in biology and is illustrated with several data sets from bioinformatics experiments.

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<p>In this thesis we study several inverse sampling procedures to test for homogeneity in a multivariate hypergeometric distribution. The procedures are finite population analogues of the procedures introduced in Panchapakesan et al. (1998) for the multinomial distribution. In order to develop some exact calculations for critical values not considered in Panchapakesan et al. we introduce some terminologies for target probabilities, transfer probabilities, potential target points, right intersection, and left union. Under the null and the alternative hypotheses, we give theorems to calculate the target and transfer probabilities, we then use these results to develop exact calculations for the critical values and powers of one of the procedures. We also propose a new approximate calculation. In order to speed up some of the calculations, we propose several fast algorithms for multiple summation.</p> <p>N >= 1680000, all the results are the same as those in the multinomial distribution.</p> <p>The computing results showed that the simulations agree closely with the exact results. For small population sizes the critical values and powers of the procedures are different from the corresponding multinomial procedures, but when</p> / Master of Science (MSc)