normalize.lvs {FLUSH.LVS.bundle}R Documentation

LVS normalization function(s)

Description

Performs the normalization step in LVS procedure.

Usage

normalize.lvs(object, ref.fun = c("median", "mean"), lvs.id, use.loess = FALSE, ...)
normalize.AffyBatch.lvs(eset, ref.fun = c("median", "mean"), lvs.id, use.loess = FALSE, ...)

Arguments

object a matrix containing unnormalized expression values.
eset an ExpressionSet or exprSet object.
ref.fun function used to compute the reference distribution. Default is median.
lvs.id The Least variant ID Probes selected after quantilic regression.
use.loess fit the normalizing curve using a smooth.spline (default) or a loess.
... ...

Value

For normalize.lvs a matrix containing LVS normalized expression values. For normalize.AffyBatch.lvs a normalized ExpressionSet.

Author(s)

Stefano Calza <calza@med.unibs.it>, Davide Valentini and Yudi Pawitan.

References

S. Calza et al. 'Normalization of oligonucleotide arrays based on the least variant set of genes' (2008, BMCBioinformatics).

See Also

lvs, compute.RA, lvs.fit

Examples

## Not run: 
# Starting from an Affybatch object called aBatch 
data.RA <- compute.RA(aBatch)
lvs.id <- lvs.fit(data.RA, proportion=0.6)
lvs.prep <- expresso(aBatch, normalize=FALSE, bgcorrect.method="mas",pmcorrect.method="mas",summary.method="mas")
normalize.AffyBatch.lvs(lvs.prep,lvs.id=lvs.id)
 
## End(Not run)

[Package FLUSH.LVS.bundle version 1.3.1 Index]