justvsn {vsn} | R Documentation |
justvsn
fits the vsn model to data
and returns an ExpressionSet
.
It is a simple wrapper for
vsn2
and predict
.
justvsn(x, reference, strata, ...) ## S4 method for signature 'RGList': justvsn(x, reference, strata, backgroundsubtract=FALSE, ...)
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. |
See vsn2
.
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.
Wolfgang Huber http://www.ebi.ac.uk/huber
##-------------------------------------------------- ## 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)