Step 1. Import Uncorrected LogRs for X and Y Chromosomes

Figure 1. Import LogR DSF window.

Figure 2. Import LogR DSF window with
DSF file selected.

Figure 3. Selecting chromosome X.

To begin, open HelixTree and create a new project. From the Project Navigator select >CNAM >Import LogR DSF. From the Import LogR DSF window (Figure 1) Browse to your LogR DSF file and click Open. All chromosomes contained within the LogR DSF will be displayed (Figure 2) under the DSF file path.

NOTE: If you are analyzing your own data, make sure the DSF file you import contains non-PCA corrected LogRs.

First import only the X chromosome. To do this click the Chromosomes button, click Uncheck All, select ‘X’ (Figure 3), and then click Ok.

Now only an ‘X’ will be displayed under the LogR DSF file path.

Click Run.

Upon import, a new spreadsheet will be created with all the X chromosome LogRs for each sample in the dataset.

NOTE: There will be quite a few spreadsheets created during this tutorial. To keep track of which is which it is good to rename your spreadsheets accordingly. To do this, from the Project Navigator Right Click on a spreadsheet’s node and select Rename Node.

If you have Y chromosome data, repeat this step selecting ‘Y’ after clicking the Chromosomes button.

There should now be two spreadsheets in the Project Navigator, one containing X chromosome LogRs and the other Y chromosome LogRs.