normalize_Rawfiles: Normalize PM Intensity values

In RLMM: A Genotype Calling Algorithm for Affymetrix SNP Arrays

Description

Given a directory with *.raw files, it will normalize the PMA and PMB intensities in each file using Xba.CQV (composite quantile vector) and return the normalized values written to *.norm files corresponding to its *.raw files. EG: If two *.raw files are used, two *.norm files will be returned. This normalization simply puts the probe data on the same scale as the training data.

Usage

normalize_Rawfiles(cqvfile = "",
                   probefiledir = getwd())

Arguments

cqvfile	Character string specifying the CQV filename (e.g., Xba.CQV) (required)
probefiledir	Character string specifying location of the *.raw files and *.norm files (optional)

Author(s)

Nusrat Rabbee <[e-mail]>, Gary Wong <[e-mail]>

RLMM documentation built on Nov. 8, 2020, 6:20 p.m.