transform_data: Finish CDF Normalization and Package Data into 1 List

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

Description

This is a helper function that finishes CDF normalization and packages all data (gene expression and phenotypic) into one simple object.

Usage

transform_data(cdfname, accession, gse, platform_id, filenamesV1)

Arguments

cdfname	Name of CDF File
accession	Accession ID corresponding to GSE object
gse	GSE object from GEOquery
platform_id	GPL platform number
filenamesV1	List of CEL file names

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

##transform_data ("hgu133ahsentrezgcdf", "11121",
## gse, "GPL570", ##c("GSM12890.CEL","GSM138290.CEL"))

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