deGenes2by2Wilcox: Function to do differential expression analysis, comparing...

In maigesPack: Functions to handle cDNA microarray data, including several methods of data analysis

Description

This function takes an object of class maiges and do differential expression analysis for the genes onto dataset, comparing only two samples, by the Wilcox (Mann-Withney) test.

Usage

deGenes2by2Wilcox(data=NULL, sLabelID=names(data@Slabels)[1], sTypeComp=NULL,
                  doClust=TRUE, ...)

Arguments

data	object of class maiges.
sLabelID	character string giving the sample label ID to be used.
sTypeComp	list with character vectors specifying the two sample types to be compared.
doClust	logical indicating if the object generated from this analysis will be used for cluster analysis. Defaults to TRUE.
...	additional parameters for functions t.test, wilcox.test or bootstrapT.

Details

This function calculate Wilcox statistics and p-values for the test comparing the equality of means using the function wilcox.test.

There another function to do parametric t test , deGenes2by2Ttest, and another option of non-parametric test doing bootstrap of t statistics, deGenes2by2BootT.

Value

The result of this function is an object of class maigesDE if doClust if FALSE or of class maigesDEcluster if it is TRUE.

Author(s)

Gustavo H. Esteves <[e-mail]>

See Also

wilcox.test, deGenes2by2Ttest and deGenes2by2BootT.

Examples

## Loading the dataset
data(gastro)

## Doing wilcoxon test fot 'Type' sample label
gastro.wilcox = deGenes2by2Wilcox(gastro.summ, sLabelID="Type")
gastro.wilcox

maigesPack documentation built on Nov. 8, 2020, 6:23 p.m.