MA: fold change versus average abundance

Compute the fold change (M) and average abundance (A) values from the data for MA plots.

Usage

analyze.ma(dataSet, ref = NULL, saveRes = TRUE)

Arguments

dataSet

A data frame containing the data signals.

ref

A character string (default = NULL) specifying the reference condition for comparison. If NULL, all pairwise comparisons are performed.

saveRes

A logical value (default = TRUE) specifying whether to save the analysis results to the current working directory.

Value

A list comprising data frames for each comparison, with each data frame containing the means of the two compared conditions for each protein, as well as the average and difference in means.