sva_modify_pvalues: Use sva's f.pvalue to adjust p-values for data adjusted by...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Use sva's f.pvalue to adjust p-values for data adjusted by combat.

Description

This is from section 5 of the sva manual: "Adjusting for surrogate values using the f.pvalue function." The following chunk of code is longer and more complex than I would like. This is because f.pvalue() assumes a pairwise comparison of a data set containing only two experimental factors. As a way to provide an example of _how_ to calculate appropriately corrected p-values for surrogate factor adjusted models, this is great; but when dealing with actual data, it falls a bit short.

Usage

sva_modify_pvalues(results)

Arguments

results

Table of differential expression results.

See Also

[sva]

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.