The CNAM copy number optimal segmenting algorithm uses log2 ratio data as input. Therefore, before you can begin copy number analysis, you must prepare a “.dsf” file of log2 data.

For the Affymetrix 500k, SNP 5.0, and SNP 6.0 arrays, CNAM supports reading CEL intensity files and calculating normalized log2 ratios for copy number segmentation and analysis in HelixTree. For details about reading CEL intensity files, see section 4.4.1.1.

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 analysis in CNAM. See Creating CNT Files using the Affymetrix CNAT Batch Analysis Tool and Creating CNCHP Files using Affymetrix Genotyping Console (Appendix C) for instructions on creating these files. Once your files have been parsed to extract the Log2 ratio values, the Copy Number Import 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 DSF log2 ratio files, see sections 4.4.1.2 and 4.4.1.3.

For the Illumina platform, you must use BeadStudio with the HelixTree DSF Plug-In to export the LogR values (i.e. log2 ratios) from your BeadStudio project. For instructions on how to install and use the plug-in, see Using the HelixTree DSF Export Plug-In in Illumina BeadStudio 3.0 (Appendix D.3). With the DSF Plug-In, you can choose to export the entire project or specific chromosomes.

You may also create a minimal data file with your own normalized log2 ratio data using the Affymetrix CNT file format. This file must contain log2 ratio data and marker map data. See Affymetrix CNT File Format (Appendix C.4) for details. You can then use the Affy CNT Conversion tool to generate a DSF of the data.

Please see the Importing Copy Number Data section (4.4) for detailed instructions for preparing a log2 ratio data file.