BlueFuse Multi: How to re center Log R Ratio (LRR) line

A user may want to re-center the Log R Ratio (LRR) line in BlueFuse Multi if a sample shows a high degree of aneuploidy (duplications and deletions). The normalization algorithm in the software attempts to establish a value for normalized intensity = 0, but the extra chromosomes may skew that calculation, and the zero value may end up actually being too high or too low for actual normal 2-copy chromosomes.

The following instructions allow the user to designate which chromosomes are 2-copy and force BlueFuse Multi to use those chromosomes for establishing the zero value against which the other chromosomes are compared.

To re-center the LRR line, perform the following steps in BlueFuse Multi:

1. Select the experiment that needs to be re-centered and select the "Edit the sample/experiment/query" button.

1. Click "Next" twice. When the following window appears, uncheck the box "Use default algorithm settings".

2. After clicking "Next", the bottom of the window shows "Chromosomes for Re-centering". The user will need to decide which chromosomes to choose for re-centering prior to this step. Looking at the chromosome profile it should be straightforward to recognize those chromosomes that appear euploid and therefore can be used as baseline.

3. Using the drop-down menu, select one or more chromosomes that you wish to use to re-center the baseline with and select the + button to add.

4. Click Next to Finish.

5. Re-analyze the sample by clicking the "BlueFuse" button on the left.

For additional information, see BlueFuse Multi v4.5 Software Guide.

For any feedback or questions regarding this article (Illumina Knowledge Article #3859), contact Illumina Technical Support [e-mail].