deSet-class {edge} | R Documentation

## The differential expression class (deSet)

### Description

The `deSet` class extends the `ExpressionSet` class. While the `ExpressionSet` class contains information about the experiment, the `deSet` class contains both experimental information and additional information relevant for differential expression analysis, explained below in Slots.

### Slots

`null.model`

  `formula`: contains the adjustment variables in the experiment. The null model is used for comparison when fitting the full model.

`full.model`

  `formula`: contains the adjustment variables and the biological variables of interest.

`null.matrix`

  `matrix`: the null model as a matrix.

`full.matrix`

  `matrix`: the full model as a matrix.

`individual`

  `factor`: contains information on which sample is from which individual in the experiment.

`qvalueObj`

  `S3 object`: containing `qvalue` object. See `qvalue` for additional details.

### Methods

`as(ExpressionSet, "deSet")`

  Coerce objects of `ExpressionSet` to `deSet`.

`lrt(deSet, ...)`

  Performs a generalized likelihood ratio test using the full and null models.

`odp(deSet, ...)`

  Performs the optimal discovery procedure, which is a new approach for optimally performing many hypothesis tests in a high-dimensional study.

`kl_clust(deSet, ...)`

  An implementation of mODP that assigns genes to modules based off of the Kullback-Leibler distance.

`fit_models(deSet, ...)`

  Fits a linear model to each gene by method of least squares.

`apply_qvalue(deSet, ...)`

  Applies `qvalue` function.

`apply_snm(deSet, ...)`

  Applies surpervised normalization of microarrays (`snm`) on gene expression data.

`apply_sva(deSet, ...)`

  Applies surrogate variable analysis (`sva`).

`fullMatrix(deSet)`

  Access and set full matrix.

`nullMatrix(deSet)`

  Access and set null matrix.

`fullModel(deSet)`

  Access and set full model.

`nullModel(deSet)`

  Access and set null model.

`individual(deSet)`

  Access and set individual slot.

`qvalueObj(deSet)`

  Access `qvalue` object. See `qvalue`.

`validObject(deSet)`

  Check validity of `deSet` object.

### Note

See `ExpressionSet` for additional slot information.

### Author(s)

John Storey, Jeffrey Leek, Andrew Bass

[Package edge version 2.12.2 Index]