Description Usage Arguments Details Value Author(s) See Also Examples
justvsn
is equivalent to calling
1 2 |
vsnrma
is a wrapper around vsn2
and rma
.
1 2 |
x |
For |
... |
Further arguments that get passed on to |
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
.
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.
vsnrma
returns an ExpressionSet
.
Wolfgang Huber
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ##--------------------------------------------------
## 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)
|
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which.max, which.min
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