Copy Number Analysis Module (CNAM)

Powerful New Methods for Whole Genome Copy Number Association Studies

CNAM is the most accurate and advanced tool for whole genome copy number association studies. Normalize your intensity data, correct for batch effects and stratification, detect copy number variations (CNVs) with lower false discoveries and greater sensitivity than any other program, and perform association analysis on found CNVs or log ratios directly.

 

  • What's New
  • Overview
  • Getting Started

New functionality added to make the copy number association workflow more complete

The following processing, analysis, and quality control measures have
been added recently to make the whole genome copy number association workflow
more complete.

weinbar View Tutorial
SNP & Variation Suite 6.1 and 6.2: New Feature Training

Whole Genome Log Ratio Association TestslogR association window
In addition to performing association tests on copy number covariates using segmentation, CNAM now offers a straightforward approach to perform whole genome single marker associations (correlation/trend, t-test, and regression) directly on log ratios. Further, a median smoothing script is available and can be applied to real-value columns (i.e. p-values) to significantly improve signal to noise ratios.
Learn more ››

Correcting for CNV-Based Batch Effects and Stratification
Similar to SNPs in HelixTree, CNAM can correct log ratios for batch effects and stratification using an Eigenstrat-based principal component analysis (PCA) method.
Learn more ››

Affymetrix 500k, 5.0, 6.0 CEL File Processing
CNAM substantially replicates the Affymetrix workflow for converting CEL files to log
ratios, including:

  • Quantile normalization (without gender bias)
  • Virtual Array Generation (merging CN and SNP data, or NSP and STY)
  • Normalizing log ratios against any reference population

This can be done for 500k, SNP 5.0, and SNP 6.0 arrays. Further, it is relatively high
speed and works for thousands of samples. (2,000 samples can be processed
overnight.) If preferred, CNAM can also read CNT and CNCHP files from Affymetrix's
CNAT Batch Analysis and Genotyping Console Software 2.0 Software tools. 
Learn more ››

What is CNAM?

CNAM provides a powerful set of novel methods and workflows for detecting CNVs and performing association analysis on both CNV covariates and log ratios directly. It employs a proprietary optimal segmenting algorithm that can detect CNVs with astonishing accuracy. In fact, its unique multivariate method can detect CNVs at single marker resolution! You can also use CNAM to normalize log ratios against a reference set of your choice and correct for batch effects and stratification in your data using an Eigenstrat-based principal component analysis method. It works on virtually unlimited sample and data sizes and is compatible with most major genotyping platforms (incl. Affymetrix 5.0 and 6.0).

Explore Further

Get Started Accelerating Your Quest for Significance!

The following resources are available to help you get started discovering significant
copy number associations in your data:

A more complete copy number association workflow

The following processing, analysis, and quality control measures have
been added recently to make the copy number association workflow more complete:

  • Download Free Trial
  • Whole Genome Association Tutorial
  • Documentation
  • Tutorials and Webinars