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 a bootstrap of t statistics method.

Usage

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deGenes2by2BootT(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 t statistics and p-values by re-sampling of the data using the function bootstrapT.

There is the option to do the t test directly, using the function deGenes2by2Ttest, or to do the non-parametric Wilcox test using the function deGenes2by2Wilcox.

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

bootstrapT, deGenes2by2Ttest and deGenes2by2Wilcox.

Examples

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## Loading the dataset
data(gastro)

## Doing bootstrap from t statistic test fot 'Type' sample label, k=1000
## specifies one thousand bootstraps
gastro.boot = deGenes2by2BootT(gastro.summ, sLabelID="Type", k=1000)
gastro.boot

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