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Basic file input parameters

This data comes from a real Plasmodium falciparum protein microarray data set measuring antibody presence from sera samples of Younger children at three different time points (C1-C3, n=5 for each conditions) from Kambila, Ghana during the malaria season. It has been shown that DNA microarray analysis techniques, like CyberT, work well on this type of data [13]. The data file is comma-delimited. The data has not been transformed. It is common to use a VSN normalization for this type of data. There is one header row. There is one label column, then five columns for condition one, then five columns for condition two, and finally five columns for condition three.

Bayes-regularized Analysis Parameters

This performs a one-way ANOVA using the Bayes-regularized variance estimates. VSN normalization is performed. PPDE analysis and multiple hypothesis testing correction are performed on the p-values. TukeyHSD pairwise post-hoc tests are performed between each condition using the Bayes-regularized variance estimates.

Non Bayes-regularized Analysis Parameters

This is equivalent to a standard one-way ANOVA using empirical variances. VSN normalization is performed. PPDE analysis and multiple hypothesis testing correction are performed on the p-values. TukeyHSD pairwise post-hoc tests are performed between each condition using the empirical variances.