Step 3. Impute Gender Based on LogR Mean Threshold

Now that appropriate thresholds have been determined for the X and Y chromosomes, you need to rerun the Row Means Threshold script, this time entering the appropriate threshold value.

For the X chromosome, open the X chromosome LogR spreadsheet and select >Scripts >Row Mean Threshold. In the first window enter the threshold determined in Step 2 and choose Greater than as the direction. On the next window choose Yes to specify a column header and then enter ‘X’ in following window.

For the Y chromosome, do the same except choose Less than as the direction in the first window and enter ‘Y’ for a column header.

The result will be two separate spreadsheets (Figures 1 and 2), again with sample names followed by two columns: mean LogRs for each sample and a binary column indicating whether the means are greater than or less than the threshold value. In both cases a ‘0’ represents male and ‘1’ female.