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]