Affymetrix Support for Copy Number Analysis

The following resources will help you get started performing copy number analysis on Affymetrix data.

Tutorials

Read the following tutorials for step-by-step workflows on how to perform copy number analysis using Affymetrix arrays:

Affymetrix GTC Browser

Processing Affymetrix CEL Files

CNAM substantially replicates the Affymetrix workflow for converting CEL files to Log2 Ratios for copy number segmentation in CNAM and association analysis in HelixTree including:

  • Quantile normalization (without gender bias)
  • Virtual Array Generation (merging CN and SNP data, or NSP and STY)
  • Normalizing Log2 Ratios against reference populations (samples can be their own reference for all platforms)

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.)

For details about reading CEL intensity files, see the section Importing Copy Number Data in the latest HelixTree Manual.

Importing Affymetrix CNT and CNCHP Files

For the Affymetrix 10K, 100K, and 500K arrays, you may use the Affymetrix CNAT Batch Analysis tool to create CNT files; or for the 100K, 500K, and SNP 6.0 arrays use Genotyping Console to create CNCHP files. These files contain normalized log2 ratios and can be converted into a DSF file for segmentation analysis in CNAM.

See Appendix C in the latest HelixTree Manual for instructions on creating CNT Files using the Affymetrix CNAT Batch Analysis Tool and Creating CNCHP Files using Affymetrix Genotyping Console

Once your files have been parsed to extract the log2 ratio values, the Copy Number Analysis Segmentation tool can be run on the resulting DSF file to create a segment means spreadsheet for analysis.

For instructions on converting your CNT and CNCHP files to log2 ratio DSF files, see the section Importing Copy Number Data in the latest HelixTree Manual.

5.0 and 6.0 Marker Maps/Annotation Files

Affymetrix 5.0 and 6.0 annotation files come in two separate files, one containing SNP probes and the other copy number probes. In order to properly process and analyze 5.0 and 6.0 data for copy number analysis you need the set merged and imported into HelixTree.

HelixTree makes this easy using the NetAffx service in the software, which you can access from the main Project Navigator window by clicking >File >Import Data >Download Affymetrix Marker Map.

Note: To properly merge the two annotation files make sure both are highlighted before clicking Download as in the figure below. If you want to automatically import the merged marker map into your project upon download, make sure to check the Import into project when downloaded box. If this box is not checked, HelixTree will download and merge the two files and then store them in your HelixTree directory. Any marker maps downloaded to this directory will show up in the bottom pane of the Download Annotations window, which you can then load into the project by clicking the Load into Project button.

Affymetrix Annotation Files

If you are having trouble downloading using the NetAffx service, you can download the following marker map files containing both SNP and CNV probes.

Note: These files may not always be up to date.

Library Files

You cannot download the library files for CNV analysis within HelixTree by using the NetAffx login, because they do not contain the information needed to process the copy number probes. Instead download the files from our website by clicking the links below.