getRatio {Starr} | R Documentation

## 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

### Author(s)

Benedikt Zacher zacher@lmb.uni-muenchen.de

### 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)

[Package Starr version 1.40.0 Index]