normalize.lvs: LVS normalization function(s)

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

Description

Performs the normalization step in LVS procedure.

Usage

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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

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## 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)

Senbee/FLUSH_LVS_bundle documentation built on May 9, 2019, 1:21 p.m.