How to calculate and import LogRDev into a GenomeStudio Project

In an existing GenomeStudio genotyping project:

1. Under the Analysis menu, select Reports, then Compute CN Metrics:

2. In the Save CN Metrics Report window, select a destination folder, enter a name for the CN Metrics file, then select Save.

3. A .csv file is created, which includes LogRDev calculations. Open the file in Microsoft Excel:

4. Format the .csv file for import into GenomeStudio:

   1. Delete Row 2 and all columns except for SampleID and LogRDev:

   2. Note that the SampleID column header has no space.

• • This is the key column that GenomeStudio will use to import the LogRDev values into the project.

    • Add a space between Sample and ID to match the GenomeStudio column header in the Samples Table: Sample ID:

1. Save the revised spreadsheet as a Tab delimited text (.txt) file.

2. In the GenomeStudio Samples Table, select the import icon:

3. In the Import window, Browse to and select the tab-delimited .txt file created, then select OK.

4. The LogRDev column will be imported into the Samples Table. If needed, click and drag the column from the far left of the table to the desired position.

Resource: GenomeStudio 2008.1 Framework User Guide (page 29, 'Importing a Column')

For any feedback or questions regarding this article (Illumina Knowledge Article #1476), contact Illumina Technical Support [e-mail].