preprocessGEO: Preprocess CEL files with SCAN

In mensxmachina/BioDataome: Functions used to preprocess datasets stored in BioDataome

Description

This function calls the SCAN method as described in Piccolo SR, Sun Y, Campbell JD, Lenburg ME, Bild AH and Johnson WE (2012). A single-sample microarray normalization method to facilitate personalized-medicine workflows. Genomics, 100(6), pp. 337-344. Example: Assuming that CEL files are located in working directory

Usage

preprocessGEO(x, y)

Arguments

x	the path where the CEL files are stored
y	the number of cores to run in parallel

Value

a matrix of dimensions: probes x samples with the normalized expression values

Examples

## Not run: 
preprocessGEO(getwd(),3) 
## End(Not run)
normCELs<-BioDataome:::normalized

mensxmachina/BioDataome documentation built on July 24, 2021, 1:05 p.m.