Computes a hierarchical differential analysis

Modified version of the limmaCompleteTest function from the DAPAR package to return both the fit and the results.

Usage

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

Arguments

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'.

Value

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.

Author

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

Examples

set.seed(2016)
data(qData)
data(sTab)
limma <- limmaCompleteTest.mod(qData, sTab, comp.type='OnevsOne')
#> Warning: Partial NA coefficients for 32 probe(s)