| 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)