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#### Basic file input parameters

This data comes from a toy DNA microarray data set of paired raw measurements.
The data file is comma-delimited.
The data has not been transformed.
We want to use VSN normalization for this data.
There is one header row.
There is one label column, and then there are five condition 1 columns and then five condition 2 columns.

- Delimiter: Commas
- Row Start: 2
- Number of label columns: 1
- Number of ratio columns: 5

#### 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: 3
- 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