Starr (version 1.28.0)

getRatio: Building ratio over experiments

Description

This function calculates the ratio over experiments.

Usage

getRatio(eSet, ip, control, description, fkt=median, featureData=F)

Arguments

eSet

An ExpressionSet, containing the logged raw intensities

ip

a boolean or integer vector, that indicate, which columns in the matrix are IP experiments

control

a boolean or integer vector, that indicate, which columns in the matrix are CONTROL or REFERENCE experiments

description

description of the new data (e.g. IPvsCONTROL)

fkt

mean or median to calculate the averaged intensity over replicates

featureData

if TRUE, featureData is added to the new ExpressionSet

Examples

##
# dataPath <- system.file("extdata", package="Starr")
# bpmapChr1 <- readBpmap(file.path(dataPath, "Scerevisiae_tlg_chr1.bpmap"))

# cels <- c(file.path(dataPath,"Rpb3_IP_chr1.cel"), file.path(dataPath,"wt_IP_chr1.cel"), 
# 	file.path(dataPath,"Rpb3_IP2_chr1.cel"))
# names <- c("rpb3_1", "wt_1","rpb3_2")
# type <- c("IP", "CONTROL", "IP")
# rpb3Chr1 <- readCelFile(bpmapChr1, cels, names, type, featureData=TRUE, log.it=TRUE)

# ips <- rpb3Chr1$type == "IP"
# controls <- rpb3Chr1$type == "CONTROL"

# rpb3_rankpercentile <- normalize.Probes(rpb3Chr1, method="rankpercentile")
# description <- c("Rpb3vsWT")
# rpb3_rankpercentile_ratio <- getRatio(rpb3_rankpercentile, ips, controls, description, fkt=median, featureData=FALSE)