justvsn: Wrapper functions for vsn

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/justvsn.R

Description

justvsn is equivalent to calling

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  fit = vsn2(x, ...)
  nx = predict(fit, newdata=x, useDataInFit = TRUE)

vsnrma is a wrapper around vsn2 and rma.

Usage

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Arguments

x

For justvsn, any kind of object for which vsn2 methods exist. For vsnrma, an AffyBatch.

...

Further arguments that get passed on to vsn2.

Details

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.

Value

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.

Author(s)

Wolfgang Huber

See Also

vsn2

Examples

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##--------------------------------------------------
## 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)

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package:BiocGenericsThe following objects are masked frompackage:parallel:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked frompackage:stats:

    IQR, mad, sd, var, xtabs

The following objects are masked frompackage: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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

vsn documentation built on Nov. 8, 2020, 8:03 p.m.