Description Usage Arguments Value Author(s) References See Also Examples
Performs the normalization step in LVS procedure.
1 2 | 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, ...)
|
object |
a matrix containing unnormalized expression values. |
eset |
an ExpressionSet or exprSet object.
ref.fun |
function used to compute the reference distribution. Default is |
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. |
... |
|
For normalize.lvs
a matrix containing LVS normalized expression values.
For normalize.AffyBatch.lvs
a normalized ExpressionSet.
Stefano Calza <calza@med.unibs.it>, Davide Valentini and Yudi Pawitan.
S. Calza et al. 'Normalization of oligonucleotide arrays based on the least variant set of genes' (2008, BMCBioinformatics).
1 2 3 4 5 6 7 8 | ## 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)
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