4. Perform Copy Number Segmentation

The next step is performing copy number segmentation on the same LogR DSF prepared/downloaded in Step 1.

From the Project Navigator select >CNAM >Copy Number Segmentation. From this window, Browse to the location where you saved the LogR DSF file and click Open. Click the Chromosomes button, click Uncheck All, check ‘22’, and then click OK.

For the purpose of this tutorial leave all other parameters as the defaults. Make sure the Univariate segmenting algorithm is selected. Univariate segmenting will segment each sample independently.

Figure 1. Copy Number Segmentation
window.

When you have finished, the Copy Number Segmentation window should look like Figure 1.

Next select the Optional Output tab (Figure 2). In this tab you will choose to export WIG files for each sample containing the segmenting results in a format that can be viewed in the Affymetrix GTC Browser.

Check the Optional Bookmark File Output box. Next, Browse to a directory where you would like to save the WIG files, click Make New Folder, name the folder HapMap_WIG, and click OK.

Figure 2. Optional Output tab.

Click Run to begin segmentation.

When CNAM has finished the segmenting process, four WIG files, one for each sample, will be saved to the directory chosen above. (If the multivariate segmenting algorithm were selected, only one WIG file would be created.) Two spreadsheets will also appear in HelixTree displaying various copy number segment information.