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. It contains the 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, for 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.

`hoffset`:

  Numeric scalar, the overall offset c- see manual page of `vsn2`.

`calib`:

  Character of length 1, see manual page of `vsn2`.

### 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

### See Also

`vsn2`

### Examples

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

[Package vsn version 3.48.1 Index]