normalizeDifferencesToAverage: Rescales channel vectors to get the same average

In HenrikBengtsson/aroma.light-BioC_release: Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types

Description

Rescales channel vectors to get the same average.

Usage

## S3 method for class 'list'
normalizeDifferencesToAverage(x, baseline=1, FUN=median, ...)

Arguments

x	A numeric list of length K.
baseline	An integer in [1,K] specifying which channel should be the baseline. The baseline channel will be almost unchanged. If NULL, the channels will be shifted towards median of them all.
FUN	A function for calculating the average of one channel.
...	Additional arguments passed to the avg function.

Value

Returns a normalized list of length K.

Author(s)

Henrik Bengtsson

Examples

# Simulate three shifted tracks of different lengths with same profiles
ns <- c(A=2, B=1, C=0.25)*1000;
xx <- lapply(ns, FUN=function(n) { seq(from=1, to=max(ns), length.out=n) });
zz <- mapply(seq(along=ns), ns, FUN=function(z,n) rep(z,n));

yy <- list(
  A = rnorm(ns["A"], mean=0, sd=0.5),
  B = rnorm(ns["B"], mean=5, sd=0.4),
  C = rnorm(ns["C"], mean=-5, sd=1.1)
);
yy <- lapply(yy, FUN=function(y) {
  n <- length(y);
  y[1:(n/2)] <- y[1:(n/2)] + 2;
  y[1:(n/4)] <- y[1:(n/4)] - 4;
  y;
});

# Shift all tracks toward the first track
yyN <- normalizeDifferencesToAverage(yy, baseline=1);

# The baseline channel is not changed
stopifnot(identical(yy[[1]], yyN[[1]]));

# Get the estimated parameters
fit <- attr(yyN, "fit");

# Plot the tracks
layout(matrix(1:2, ncol=1));
x <- unlist(xx);
col <- unlist(zz);
y <- unlist(yy);
yN <- unlist(yyN);
plot(x, y, col=col, ylim=c(-10,10));
plot(x, yN, col=col, ylim=c(-10,10));

HenrikBengtsson/aroma.light-BioC_release documentation built on May 7, 2019, 1:55 a.m.