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Analyzing summarized data

Source: R/analyze.R
analyze.Rd

Apply a statistical test to the data.

Usage

analyze(dataSet, conditions, testType = "t-test")

Arguments

dataSet

The 2d data set of data.

conditions

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 dataSet and this argument is not specified, the conditions will automatically be selected by sorting the unique values alphabetically and in ascending order.

testType

A string (default = "t-test") specifying which statistical test to use:

  1. "t-test": Unequal variance t-test.

  2. "mod.t-test": Moderated t-test (Smyth 2004) .

  3. "MA": Output to plot an MA plot.

Value

A 2d dataframe includes the following information:

  • "t-test" or "mod.t-test": The differences in means and P-values for each protein between the two conditions.

  • "MA": Protein-wise averages within each condition.

Details

The second condition serves as the reference for comparison.

  • "t-test" and "mod.t-test": The differences are calculated by subtracting the mean of the second condition from the mean of the first condition (Condition 1 - Condition 2).

  • "MA": The rows are ordered by conditions. Specifically, the first row corresponds to the protein-wise average of the first condition, and the second row corresponds to the second condition.

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 .