Factorial designed microarray experiment analysis


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contrastTest 'contrastTest' performs simultaneous tests of linear contrasts on the parameters estimates from a linear model.
estrogen Microarray Data from an Experiment on Breast Cancer Cells
findFC A function to find the fold change between two experimental conditions in a factorial experiment based on the linear model parameter estimates.
findFClog A function to find the fold change between two experimental conditions in a factorial experiment based on the linear model parameter estimates for the data that has been log-transformed.
kRepsOverA A filter function for at least k sets of replicates in a factorial experiment to have mean larger than A.
madOutPair A function to determine if the pair with the largest difference between replicates is the result of a single outlier.
outlierPair A method for detecting single outliers in experimental designs with only two replicates per treatment condition.
par2lambda A function to construct the appropriate lambda matrix for a test of contrast of linear model parameters.