MiChip (version 1.26.0)

workedExampleMedianNormalize: Worked Example of MiChip Processing

Description

Loads a set of hybridizations into a matrix and them proceeds to filter, summarize and median normalize them

Usage

workedExampleMedianNormalize(exptname, intensityCutoff=0, datadir=".", minSumlength, madAdjust = FALSE)

Arguments

exptname

string indicating the name of the experiment

intensityCutoff

The intensity value for accepting the spots intensity value in the experiment

datadir

The directory where hybridization files are found.

minSumlength

Minimum exceptable number of values to summarize intensity value.

madAdjust

if TRUE then summarized data will be filtered according to the MAD median absolute deviation and set to NA if the median is less than MAD

Examples

#Normalize data in the current directory to the median per chip
datadir <- system.file("extdata", package="MiChip")
myNormedEset <-workedExampleMedianNormalize("MyExpt", intensityCutoff=0, datadir, minSumlength=0, madAdjust=TRUE)