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]