justvsn {vsn} | R Documentation |
justvsn
returns the vsn-normalised intensities in
an object generally of the same class as its first
argument (see the man page of predict
for
details). It preserves the metadata. It is equivalent to calling
fit = vsn2(x, ...) nx = predict(fit, newdata=x, useDataInFit = TRUE)
vsnrma
is a wrapper around vsn2
and rma
justvsn(x, ...) vsnrma(x, ...)
x |
For justvsn , any kind of object for which
vsn2 methods exist.
For vsnrma , an
AffyBatch . |
... |
Further arguments that get passed on to vsn2 . |
vsnrma
does probe-wise
background correction and between-array normalization by calling
vsn2
on the perfect match (PM) values only. Probeset
summaries are calculated with the medianpolish algorithm of
rma
.
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 RGList ##-------------------------------------------------- rg = new("RGList", list(R=exprs(kidney)[,1,drop=FALSE], G=exprs(kidney)[,2,drop=FALSE])) erge = justvsn(rg)