Function to do differential expression analysis, comparing only two samples

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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

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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 <gesteves@vision.ime.usp.br>

See Also

wilcox.test, deGenes2by2Ttest and deGenes2by2BootT.

Examples

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## Loading the dataset
data(gastro)

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

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