normalize.lvs {FLUSH.LVS.bundle} | R Documentation |
Performs the normalization step in LVS procedure.
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 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. |
... |
... |
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).
## 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)