vsn2trsf {vsn}R Documentation

Apply the vsn transformation to data

Description

Apply the vsn transformation to data.

Usage

## S4 method for signature 'vsn':
predict(object, newdata, log2scale=TRUE)
vsn2trsf(x, p, strata)

Arguments

object An object of class vsn that contains transformation parameters and strata information, typically this is the result of a previous call to vsn2.
newdata Numeric matrix, vector or ExpressionSet with the data to which an existing fit is to be applied to. A typical use case is when the fit is made to a set of control features and then the transformation is to be applied to the full set of data. If newdata is a vector, it is considered a matrix with one column and nrow(newdata) rows.
log2scale If TRUE, the data are returned on the glog scale to base 2, and an overall offset c is added (see Value section of the vsn2 manual page). If FALSE, the data are returned on the glog scale to base e, and no offset is added.
x Numeric matrix.
p An array with the transformation parameters. If strata is specified, p is expected to be a 3d array, the first dimension corresponds to the levels of strata, the second dimension to the columns of x and the third dimension must be 2, corresponding to offsets and factors. If strata is missing, then the first dimension may be omitted and p can be a 2d array. NA values are not allowed.
strata optional, a factor whose length is nrow(x). Can be used for stratified normalization (i.e. separate offsets a and factors b for each level of strata).

Value

For vsn2trsf, a matrix of the same size as x. For predict, a matrix if newdata was a matrix, and an ExpressionSet, newdata was an ExpressionSet. Dimnames and metadata are preserved.

Author(s)

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

Examples

data("kidney")
param = array(c(-0.1, -0.1, 0.003, 0.003), dim=c(1,2,2))
tk = vsn2trsf(exprs(kidney), param)
plot(tk, pch=".")

## see also the 'subsample' argument of vsn for an easier way to do this:
fit = vsn2(kidney[sample(nrow(kidney), 500), ])
tn = predict(fit, newdata=exprs(kidney))


[Package vsn version 2.2.0 Index]