vsn {vsn}R Documentation

Class to contain result of a vsn fit

Description

Class to contain result of a vsn fit

Creating Objects

new("vsn") vsn2(x) with x being an ExpressionSet.

Slots

coefficients:
A 3D array of size (number of strata) x (number of columns of the data matrix) x 2 containing fitted normalization parameters (see vignette).
strata:
A factor of length 0 or n. If its length is n, then its levels correspond to different normalization strata (see vignette).
mu:
A numeric vector of length n with the fitted parameters $hat{μ}_k$, $k=1,...,n$.
sigsq:
A numeric scalar, $hat{σ}^2$.
hx:
A numeric matrix with 0 or n rows. If the number of rows is n, then hx contains the transformed data matrix.
lbfgsb:
An integer scalar containing the return code from the L-BFGS-B optimizer.

Methods

[
Subset
dim
Get dimensions of data matrix.
nrow
Get number of rows of data matrix.
ncol
Get number of columns of data matrix.
show
Print a summary of the object
exprs
Accessor to slot hx.
coef, coefficients
Accessors to slot coefficients.

Author(s)

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

See Also

vsn2

Examples

  data("kidney")
  v = vsn2(kidney)
  show(v)
  dim(v)
  v[1:10, ]

[Package vsn version 3.8.0 Index]