deSet {edge} | R Documentation

## Create a deSet object from an ExpressionSet

### Description

Creates a `deSet` object that extends the `ExpressionSet` object.

### Usage

    deSet(object, full.model, null.model, individual = NULL)

    ## S4 method for signature 'ExpressionSet'
    deSet(object, full.model, null.model,
      individual = NULL)

### Arguments

`object` | `S4 object`: `ExpressionSet`
`full.model` | `formula`: full model containing the both the adjustment and the biological variables for the experiment.
`null.model` | `formula`: null model containing the adjustment variables for the experiment.
`individual` | `factor`: information on repeated samples in experiment.

### Value

`deSet` object

### Note

It is essential that the null and full models have the same variables as the ExpressionSet phenoType column names.

### Author(s)

John Storey, Andrew Bass

### See Also

`deSet`, `odp` and `lrt`

### Examples

    # import data
    library(splines)
    data(kidney)
    age <- kidney$age
    sex <- kidney$sex
    kidexpr <- kidney$kidexpr
    cov <- data.frame(sex = sex, age = age)
    pDat <- as(cov, "AnnotatedDataFrame")
    exp_set <- ExpressionSet(assayData = kidexpr, phenoData = pDat)

    # create models
    null_model <- ~sex
    full_model <- ~sex + ns(age, df = 4)

    # create deSet object from data
    de_obj <- deSet(exp_set, null.model = null_model,
    full.model = full_model)

    # optionally add individuals to experiment, in this case there are 36
    # individuals that were sampled twice
    indSamples <- as.factor(rep(1:36, each = 2))
    de_obj <- deSet(exp_set, null.model = null_model,
    full.model = full_model, ind = indSamples)
    summary(de_obj)

[Package edge version 2.19.0 Index]