getDecideTests {AgiMicroRna} | R Documentation

## Differential expression analysis an multiplicity of the tests

### Description

It Uses the `decideTests` function of the 'limma' package to classify the list of genes as up, down or not significant after correcting by the multiplicity of the tests.

### Usage

    getDecideTests(fit2, DEmethod, MTestmethod, PVcut,verbose=FALSE)

### Arguments

`fit2` | MArrayLM object
`DEmethod` | method for `decideTests`, only 'separate' or 'nestedF' are implemented. see `decideTests` in limma package.
`MTestmethod` | method for multiple test, choices are 'none','BH', 'BY', ... see `p.adjust`
`PVcut` | p value threshold to declare significant features
`verbose` | logical, if `TRUE` prints out output

### Value

A 'TestResults' object of the 'limma' package It prints out the number of UP and DOWN genes for every contrasts according to the p value limit specified

### Author(s)

Pedro Lopez-Romero

### References

Smyth, G. K. (2005). Limma: linear models for microarray data. In: 'Bioinformatics and Computational Biology Solutions using R and Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds), Springer, New York, pages 397–420.

### See Also

An overview of miRNA differential expression analysis is given in `basicLimma`

### Examples

    ## Not run:
    DE=getDecideTests(fit2,
            DEmethod="separate",
            MTestmethod="BH",
            PVcut=0.10,
    	verbose=TRUE)

    ## End(Not run)

[Package AgiMicroRna version 2.38.0 Index]