justvsn {vsn}R Documentation

Normalization with vsn

Description

justvsn fits the vsn model to data and returns an ExpressionSet. It is a simple wrapper for vsn2 and predict.

Usage

justvsn(x, reference, strata, ...)

## S4 method for signature 'RGList':
justvsn(x, reference, strata, backgroundsubtract=FALSE, ...)

Arguments

x An object containing the data to which the model is to be fitted. Methods exist for ExpressionSet, AffyBatch (from the affy package) and RGList (from the limma package).
reference, strata, ... As in vsn2.
backgroundsubtract Logical of length 1, it applies only to the method for RGList objects and indicates whether local background estimates in the Rb and Gb slots of x should be subtracted before fitting vsn.

Details

See vsn2.

Value

An ExpressionSet.
If x is an ExpressionSet, then the dimensions and the metadata of the returned object will be the same, and its matrix of expression values are the normalized and transformed version of the input.
If x is an AffyBatch, probe-wise background correction and between-array normalization are done by vsn2 on the perfect match (PM) values only. Probeset summaries are calculated with the medianpolish algorithm of rma.
If x is an RGList, then vsn2 is applied to the matrix cbind(x$R, x$G). If backgroundsubtract=TRUE, then cbind(x$Rb, x$Gb) is subtracted before.

Author(s)

Wolfgang Huber http://www.ebi.ac.uk/huber

See Also

vsn2

Examples

##--------------------------------------------------
## use "vsn2" to produce a "vsn" object
##--------------------------------------------------
data("kidney")
fit = vsn2(kidney)
nkid = predict(fit, newdata=kidney)

##--------------------------------------------------
## justvsn on ExpressionSet
##--------------------------------------------------
nkid2 = justvsn(kidney)
stopifnot(identical(exprs(nkid), exprs(nkid2)))

##--------------------------------------------------
## justvsn on AffyBatch
##--------------------------------------------------
data("affybatch.example")
data("cdfenv.example")
eabe = justvsn(affybatch.example)

##--------------------------------------------------
## justvsn on RGList
##--------------------------------------------------
rg = new("RGList", list(R=exprs(kidney)[,1,drop=FALSE], G=exprs(kidney)[,2,drop=FALSE]))
erge = justvsn(rg)

[Package vsn version 2.2.0 Index]