runCdfCode: CDF Normalize Data

In anjanbharadwaj/GEOpipeline: GEOpipeline: Streamlined Pipeline for Automatically CDF Normalizing Microarray Datasets

Description

This is a helper function that uses the ReadAffy function based on the CDF found and the gene expression data provided (in the format of CEL files) .

Usage

runCdfCode(data, wd,accession,cdfname, platform_id)

Arguments

data	GSE object from GEOquery
wd	Working directory filepath
accession	Accession ID corresponding to GSE object
cdfname	Name of CDF File
platform_id	GPL platform number

Value

expression	The normalized gene expression data
phenotype_data	The corresponding phenotype metadata for each of the samples in the gene expression data

Author(s)

Anjan Bharadwaj

Examples

##runCdfCode (data, "/Users/johndoe/Documents/GEODATA/##GSE11121",
##"11121","hgu133ahsentrezgcdf", "GPL570")

anjanbharadwaj/GEOpipeline documentation built on Nov. 2, 2019, 1:54 p.m.