Intensity.Norm {anapuce}R Documentation

Function to compute normalized intensity for each channel

Description

Computes normalized intensity for each channel and each array from the file containing normalized data.

Usage

Intensity.Norm(fileIN = "resNorm.txt", n = 3, ind.array = NULL, name.A = "A", name.M = "M.norm", sep = "\t", center = FALSE, log.transf = TRUE, ...)

Arguments

fileIN input dataframe.
n number of identificant columns.
ind.array indices of arrays to use.
name.A character string containing a regular expression contained in the columnames corresponding to the A values.
name.M character string containing a regular expression contained in the columnames corresponding to the M values.
sep the field separator string to use in the read.table function.
center logical indicating wether data will be centered by array.
log.transf logical indicating wether data will stay log-transformed.
... Further arguments to be passed to read.table.

Value

A R dataframe containing the n first columns of the input dataframe and the "normalized" intensity for the red and green channels of each chosen array.

Author(s)

J. Aubert

References

Thorne, N.P. (2004) Single-channel normalisation and analysis of twocolour cDNA microarray data, PhD thesis

See Also

normalisation


[Package anapuce version 2.1 Index]