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Preparing Log2 Ratio Data

10.2 Preparing Log2 Ratio Data

The CNAM optimal segmenting algorithm uses log2 ratio data as input. Therefore, before you can begin copy number analysis, you must import log2 data into an SVS project.

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 SVS. For details about reading CEL intensity files, see Affymetrix CEL 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 imported into SVS for analysis in CNAM. See Affymetrix Files for instructions on creating and importing these files. Once the files have been parsed to extract the log2 ratio values, the data is ready for copy number analysis.

For the Illumina platform, you must use GenomeStudio with the SVS DSF Export Plug-In to export the log2 ratio values from your GenomeStudio project. For instructions on how to install and use the plug-in, see Exporting Data from GenomeStudio.

For the Agilent platform, you must use the Agilent import menu item and select the correct intensity field for importing the log2 ratio data. See Agilent Files for more information.

For the NimbleGen platform, you must use the NimbleGen Data Summary Files import menu item and select at least one field to import. See NimbleGen Data Summary Files for more information.

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 for details. You can then import the Affymetrix CNT files to create a spreadsheet of log2 ratio data.