deSet: Create a deSet object from an ExpressionSet

Description Usage Arguments Value Note Author(s) See Also Examples

Description

Creates a deSet object that extends the ExpressionSet object.

Usage

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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

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# 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)


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