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 t test.

Usage

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deGenes2by2Ttest(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 function t.test.

Details

This function calculate t statistics and p-values for the test of difference in the means of the groups using the function t.test.

There are other two functions, deGenes2by2Wilcox and deGenes2by2BootT, to do non-parametric tests by the Wilcox test an t statistic bootstrap, respectively.

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

t.test, deGenes2by2Wilcox and deGenes2by2BootT.

Examples

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## Loading the dataset
data(gastro)

## Doing t test fot 'Type' sample label
gastro.ttest = deGenes2by2Ttest(gastro.summ, sLabelID="Type")
gastro.ttest

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