ExpressionSetList-class {XDE} | R Documentation

## A class for containing a list of ExpressionSets

### Description

Each element in the list must be a valid `ExpressionSet`. The `featureNames` must be identical for each `ExpressionSet`.

### Objects from the Class

Objects can be created by calls of the form `new("ExpressionSetList", ...)`.

### Slots

`.Data`:
  Object of class `"list"`

### Extends

Class `"list"`, from data part. Class `"vector"`, by class "list", distance 2. Class `class.AssayData`, by class "list", distance 2.

### Methods

.integrativeCorrelationFilter
  `signature(object = "ExpressionSetList")` Experimental function for filtering an arbitrary list of ExpressionSets by integrative correlation. Genes are excluded that do not exceed the fdr threshold in at least 1 of the studies.
"["
  `signature(x = "ExpressionSetList")` Subsets each `ExpressionSet` element in the list.
coerce
  `signature(from = "list", to = "ExpressionSetList")` Coerces a list of `ExpressionSet` objects to an object of class `ExpressionSetList`. The `validityMethod` for the `ExpressionSetList` class will return an error if the `featureNames` for each `ExpressionSet` are not identical.
featureNames
  `signature(object = "ExpressionSetList")` Accessor for the `featureNames`
geneCenter
  `signature(object = "ExpressionSetList")` See `geneCenter`
lapply
  `signature(object="ExpresssionSetList")` Coerces instance of ExpressionSetList to a list and does lapply on the list. Returns an object of class ExpressionSetList
nSamples
  `signature(x = "ExpressionSetList")` Numerical vector giving the number of samples in each `ExpressionSet`
nrow
  `signature(x = "ExpressionSetList")` Numerical: number of features or genes
pData
  `signature(object = "ExpressionSetList")` returns a list of `data.frames`. The elements of the list correspond to the studies in the `ExpressionSetList` object.
.pca
  `signature(object = "ExpressionSetList")` Runs principal components to generate cross-study summary scores of differential expression in multiple studies. Not meant to be called directly. See `xsScores`.
standardizeSamples
  `signature(object = "ExpressionSetList")` See `standardizeSamples`
studyCenter
  `signature(object = "ExpressionSetList")` See `studyCenter`
xapply
  `signature(object="ExpressionSetList")` An lapply for `ExpressionSetList` instances. See `xapply`.
zeroNu
  `signature(object = "ExpressionSetList")` See ``zeroNu`.

### Author(s)

R. Scharpf

### See Also

`XdeMcmc-class`, `XdeParameter-class`

### Examples

    showClass("ExpressionSetList")
    data(expressionSetList)

[Package XDE version 1.0.0 Index]