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Full-Text Articles in Computational Biology
Genome Scanning Methods For Comparing Sequences Between Groups, With Application To Hiv Vaccine Trials, Peter B. Gilbert, Chunyuan Wu, David V. Jobes
Genome Scanning Methods For Comparing Sequences Between Groups, With Application To Hiv Vaccine Trials, Peter B. Gilbert, Chunyuan Wu, David V. Jobes
UW Biostatistics Working Paper Series
Consider a placebo-controlled preventive HIV vaccine efficacy trial. An HIV amino acid sequence is measured from each volunteer who acquires HIV, and these sequences are aligned together with the reference HIV sequence represented in the vaccine. We develop genome scanning methods to identify HIV positions at which the amino acids in sequences from infected vaccine recipients tend to be more divergent from the corresponding reference amino acid than the amino acids in sequences from infected placebo recipients. We consider five two-sample test statistics, based on Euclidean, Mahalanobis, and Kullback-Leibler divergence measures. Weights are incorporated to reflect biological information contained in …
2^K Factorials In Blocks Of Size 2, With Application To Two-Color Microarray Experiments, Kathleen F. Kerr
2^K Factorials In Blocks Of Size 2, With Application To Two-Color Microarray Experiments, Kathleen F. Kerr
UW Biostatistics Working Paper Series
When a two-level design must be run in blocks of size two, there is a unique blocking scheme that enables estimation of all the main effects. Unfortunately this design does not enable estimation of any two-factor interactions. When the experimental goal is to estimate all main effects and two-factor interactions, it is necessary to combine replicates of the experiment that use different blocking schemes. In this paper we identify such designs for up to eight factors that enable estimation of all main effects and two-factor interactions with the fewest number of replications. In addition, we give a construction for general …