DAPAR (version 1.4.7)

limmaCompleteTest: Computes a hierarchical differential analysis

Description

This function is a limmaCompleteTest

Usage

limmaCompleteTest(qData, Conditions, RepBio, RepTech, Contrast = 1)

Arguments

qData

A matrix of quantitative data, without any missing values.

Conditions

A vector of factor which indicates the name of the biological condition for each replicate.

RepBio

A vector of factor which indicates the number of the bio rep for each replicate.

RepTech

A vector of factor which indicates the number of the tech rep for each replicate.

Contrast

Indicates if the test concists of the comparison of each biological condition versus each of the other ones (Contrast=1; for example H0:"C1=C2" vs H1:"C1!=C2", etc.) or each condition versus all others (Contrast=2; e.g. H0:"C1=(C2+C3)/2" vs H1:"C1!=(C2+C3)/2", etc. if there are three conditions).

Value

fdsfdgfdg

Examples

data(UPSpep25)
obj <- wrapper.mvImputation(UPSpep25, "QRILC")
condition1 <- '25fmol'
condition2 <- '10fmol'
qData <- Biobase::exprs(obj)
RepBio <- RepTech <- factor(1:6)
conds <- factor(c(rep(condition1, 3), (rep(condition2, 3))))
limma <- limmaCompleteTest(qData,conds,RepBio, RepTech)