normalize_Rawfiles

Character string specifying the CQV filename (e.g., Xba.CQV) (required)

cqvfile

Character string specifying location of the *.raw files and *.norm files (optional)

probefiledir


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.


manip

A classification algorithm, based on a multi-chip, multi-SNP
approach for Affymetrix SNP arrays. Using a large training sample where the
genotype labels are known, this aglorithm will obtain more accurate
classification results on new data. RLMM is based on a robust, linear model
and uses the Mahalanobis distance for classification. The chip-to-chip
non-biological variation is removed through normalization. This model-based
algorithm captures the similarities across genotype groups and probes, as
well as thousands other SNPs for accurate classification.
NOTE: 100K-Xba only at for now.

Nusrat Rabbee

RLMM

A Genotype Calling Algorithm for Affymetrix SNP Arrays

normalize_Rawfiles function

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.

normalize_Rawfiles: Normalize PM Intensity values

Description

Usage

Arguments