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#### Basic file input parameters

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 analyzed the sera of children who did (n=29) and did not (n=12)
have a clinical malaria episode in the following malaria season.
For illustrative purposes, this dataset is a subset of two data points each from the malaria positive
and malaria negative children.

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 2 columns for the malaria positive children and then
2 columns for the malaria negative children.

- Delimiter: Commas
- Row Start: 2
- Number of label columns: 1
- Number of first condition columns: 2
- Number of second condition columns: 2

#### Bayes-regularized Analysis Parameters

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.

- Normalization: VSN
- Bayes Sliding Window: 101
- Bayes Confidence: 6
- Run PPDE: checked
- Run Multiple Hypothesis Testing Correction: checked

#### Non Bayes-regularized Analysis Parameters

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.

- Normalization: VSN
- Bayes Confidence: BLANK (Default)
- Run PPDE: checked
- Run Multiple Hypothesis Testing Correction: checked