This data comes from a previously published protein microrray study of the natural immune response to Plasmodium falciparum [10]. The array consists of 2,320 probes. The specific analysis is looking at the sera of children who did (n=29) and did not (n=12) have a clinical malaria episode in the following malaria season.
It has been shown that DNA microarray analysis techniques, like Cyber-T, 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, and then there are 29 columns for the malaria positive children and then 12 columns for the malaria negative children.
This performs a two-sample t-test using the Bayes-regularized variance estimates. The data is normalized using VSN. PPDE analysis and multiple hypothesis testing correction are performed on the p-values.
This is equivalent to a standard t-test using empirical variances. The data is normalized using VSN. PPDE analysis and multiple hypothesis testing correction are performed on the p-values.