EBAM.Anal: EBAM Fudge Factor

In flajole/MApckg: R package of MetaboAnalyst functions

Description

EBAM.A0.Anal - finds EBAM Fudge Factor. Uses find.a0 function.

EBAM.Cmpd.Anal - performs Empirical Bayesian Analysis of Microarray (and Metabolites). Uses ebam function.

Usage

EBAM.A0.Anal(dataSet, analSet, paired = FALSE, var.equal = TRUE)

EBAM.Cmpd.Anal(dataSet, analSet, method = "z.ebam", A0 = 0,
  paired = FALSE, var.equal = TRUE)

Arguments

dataSet	List, data set object generated by MS_to_MA function.
analSet	List, containing the results of statistical analysis (can be just an empty list).
paired	Are values in data set paired or not.
var.equal	Are variances assumed equal or not.
method	A character string or name specifying the method or function that should be used in the computation of the expression score z. If "z.ebam", a modified t- or F-statistic, respectively, will be computed as proposed by Efron et al. (2001). If "wilc.ebam", a (standardized) Wilcoxon sum / signed rank statistic will be used as expression score. Note: if method is "wilc.ebam", then A0 and var.equal parameters will be ignored
A0	Fudge Factor. EBAM.A0.Anal

Value

EBAM.A0.Anal - native analSet with one added $ebam.a0 element containing standard find.a0 function output

EBAM.Cmpd.Anal - native analSet with one added $ebam element containing standard ebam function output

Functions

• EBAM.A0.Anal: Find EBAM Fudge Factor.

See Also

ebam, find.a0 for used statistical functions
SetEBAMSigMat for setting matrix of significance
PlotEBAM for plotting functions

flajole/MApckg documentation built on May 16, 2019, 1:16 p.m.