Moderated t-test

Apply moderated t-test (Smyth 2004) to the data.

Usage

mod_t_test(dataSet, condCol = "merged_condition", cond)

Arguments

dataSet

A data frame containing the data signals.

condCol

A string (default = "merged_condition") specifying the column name in dataSet that contains the conditions to compared.

cond

A string specifying which two conditions to compare. The order is important, as the second condition serves as the reference for comparison. When there are two conditions in condCol of dataSet and this argument is not specified, the cond will automatically be selected by sorting the unique values alphabetically and in ascending order.

Value

A data frame containing the differences in means and p-values for each compound between the two conditions.

Details

The second condition serves as the reference for comparison. The differences are calculated by subtracting the mean of the second condition from the mean of the first condition (Condition 1 - Condition 2).

References

Smyth GK (2004). “Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments.” Statistical Applications in Genetics and Molecular Biology, 3(1). doi:10.2202/1544-6115.1027 .