limmaCompleteTest: Computes a hierarchical differential analysis
In DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

Description Usage Arguments Value Author(s) Examples

This function is a limmaCompleteTest

1	limmaCompleteTest(qData, sTab, comp.type = "OnevsOne")

`qData`	A matrix of quantitative data, without any missing values.
`sTab`	A dataframe of experimental design (pData()).
`comp.type`	A string that corresponds to the type of comparison. Values are: 'anova1way', 'OnevsOne' and 'OnevsAll'; default is 'OnevsOne'.

A list of two dataframes : logFC and P_Value. The first one contains the logFC values of all the comparisons (one column for one comparison), the second one contains the pvalue of all the comparisons (one column for one comparison). The names of the columns for those two dataframes are identical and correspond to the description of the comparison.

Hélène Borges, Thomas Burger, Quentin Giai-Gianetto, Samuel Wieczorek

utils::data(Exp1_R25_pept, package='DAPARdata')
obj <- Exp1_R25_pept
qData <- Biobase::exprs(obj)
sTab <- Biobase::pData(obj)
limma <- limmaCompleteTest(qData, sTab, comp.type='anova1way')