pvalHistogram {AgiMicroRna} | R Documentation

## Histogram of the p values

### Description

Creates an histogram of the pvalues. For multiple contrats, creates an histogram for every t.test pvalue (separate) or a single histogram for the F.test pvalue (nestedF). A uniform histogram will indicate no differential expression in the data set, whereas a right skewed histogram, will indicate some significant differential expression

### Usage

    pvalHistogram(fit2, DE, PVcut, DEmethod, MTestmethod, CM,verbose=FALSE)

### Arguments

`fit2` | MArrayLM object
`DE` | TestResults object
`PVcut` | limit p value to declare significant features
`DEmethod` | method for decideTests, only 'separate' or 'nestedF' are implemented
`MTestmethod` | method for multiple test
`CM` | contrast matrix
`verbose` | logical, if `TRUE` prints out output

### Author(s)

Pedro Lopez-Romero

### See Also

An overview of miRNA differential expression analysis is given in `basicLimma` An example of how to get the 'TestResults' object is in `getDecideTests`

### Examples

    ## Not run:
    pvalHistogram(fit2,DE,PVcut=0.10,
         DEmethod="separate",MTestmethod="BH",CM)

    ## End(Not run)

[Package AgiMicroRna version 2.42.0 Index]