calculateTtest {puma} | R Documentation

## Calculate differential expression between conditions using T-test

### Description

Automatically creates design and contrast matrices if not specified. This function is useful for comparing T-test results with those of other differential expression (DE) methods such as `pumaDE`.

### Usage

    calculateTtest(
    	eset
    ,	design.matrix = createDesignMatrix(eset)
    ,	contrast.matrix = createContrastMatrix(eset)
    )

### Arguments

`eset` | An object of class `ExpressionSet`
`design.matrix` | A design matrix
`contrast.matrix` | A contrast matrix

### Details

The `eset` argument must be supplied, and must be a valid `ExpressionSet` object. Design and contrast matrices can be supplied, but if not, default matrices will be used. These should usually be sufficient for most analyses.

### Value

An object of class `DEResult`.

### Author(s)

Richard D. Pearson

### See Also

Related methods `pumaDE`, `calculateLimma`, `calculateFC`, `createDesignMatrix` and `createContrastMatrix` and class `DEResult`

### Examples

    	eset_test <- new("ExpressionSet", exprs=matrix(rnorm(400,8,2),100,4))
    	pData(eset_test) <- data.frame("class"=c("A", "A", "B", "B"))
    	TtestRes <- calculateTtest(eset_test)
    	plotErrorBars(eset_test, topGenes(TtestRes))

[Package puma version 3.26.0 Index]