normalize.loess {codelink}R Documentation

Normalized chips using cyclic loess.

Description

Takes a matrix and apply cyclic loess normalization. It is based in normalize.loess from package affy but supports NA.

Usage

  normalize.loess(mat, subset = sample(1:(dim(mat)[1]), 
    min(c(5000, nrow(mat)))), epsilon = 10^-2, maxit = 1, log.it = TRUE,
        verbose = FALSE, span = 2/3, family.loess = "symmetric", weights = NULL)

Arguments

mat a matrix with columns containing the values of the chips to normalize.
subset a subset of the data to fit a loess to.
epsilon a tolerance value (supposed to be a small value - used as a stopping criterium).
maxit maximum number of iterations.
log.it logical. If TRUE it takes the log2 of mat
verbose logical. If TRUE displays current pair of chip being worked on.
span parameter to be passed the function loess
family.loess parameter to be passed the function loess. "gaussian" or "symmetric" are acceptable values for this parameter.
weights a vector of weights for the individual measurements.

Details

Value

A matrix of normalized values.

Note

Author(s)

Diego Diez

See Also

Examples

## Not run: 
        mat <- matrix(sample(500), 100, 5)
        mat <- normalize.loess(mat)
## End(Not run)

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