apt_cytoscan_process: Normalize CytoScanHD_Array arrays using Affymetrix Power...

In gustaveroussy/apt.cytoscan.2.4.0: Affymetrix CytoScan processing using apt-copynumber-cyto-ssa (2.4.0)

Normalize CytoScanHD_Array arrays using Affymetrix Power Tools.

Description

This function performs the normalization of CEL file list for Affymetrix CytoScanHD_Array microarrays using the binary apt-copynumber-cyto-ssa (v2.4.0 2015-08-28) from Affymetrix Power Tools.

Usage

apt.cytoscan.process(CEL = NULL, samplename = NULL, dual.norm = FALSE,
normal.diploid = FALSE, out.dir = getwd(), temp.files.keep = FALSE,
force.OS = NULL, apt.build = "na33.r4")

Arguments

CEL	A CEL file.
samplename	Name of the analyzed sample.
dual.norm	Perform a dual-channel normalization (recommended for a better wave-effect bias normalization).
normal.diploid	Consider the sample as normal-diploid (not recommended for tumors).
out.dir	The path to output results.
temp.files.keep	Keep the (numerous) intermediate files.
force.OS	Specifiy the OS type of the execution machine (see Details).
apt.build	Affymetrix genome build version.

Details

CEL.list.file is a tab-separated text file containing 2 columns :

• cel_files : Name (and path) of the CEL file(s)

• SampleName : The output sample name

Output files (all begin with the sample name as a prefix) :

• '*.OSCHP' : Contains the processed data. This format actually internaly is HDF5 [TO UPDATE!!].

force.OS is NULL by default, but can take any of these values :

• linux

• windows

• osx

Author(s)

Bastien Job

gustaveroussy/apt.cytoscan.2.4.0 documentation built on July 10, 2024, 3:46 p.m.