3. Convert LogRs to CNT Files

Once the marker map is loaded, the next step is to convert LogRs prepared/downloaded in Step 1 to CNT files. CNT files are proprietary Affymetrix files which are tab delimited and contain information for each marker such as its marker name, chromosome, physical position, and intensity value.

In SVS version 6.4 a new option was added to the CNAM menu enabling you to save a LogR DSF directly to CNT files, one for each sample in your dataset. This is a much more efficient option than previously supported as it eliminates having to first import logRs into HelixTree (as outlined in previous tutorials) and can accommodate converting an entire LogR DSF file for virtually unlimited sample sizes.

To run this option select >CNAM >Save LogR DSF to CNT Files from the Project Navigator. The window in Figure 1 will appear.

From here, Browse to the four sample LogR DSF prepared/downloaded in Step 1 and click Open. A list of all chromosomes in the DSF will appear under the file path. For this tutorial only convert Chromosome 22. To do this, click the Chromosomes button, click Uncheck All, check ‘22’, and then click OK.

Next, go to the Output tab. Choose a directory to save the CNT files. Ignore the Exclude Markers tab for the purpose of this tutorial. Click Run.

The result will be four CNT files in the directory you provided.