# 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.\
   ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-d852571800d531307ba68879b4f36ce0b2f2f18a%2Fimage1.jpg?alt=media)

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-399dfba2e5cc7e4a00855add6b14d9e2716cfab5%2Fimage2.jpg?alt=media)

2. Click "**Next**" twice. When the following window appears, **uncheck** the box "**Use default algorithm settings**". ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-5eb94fdc53efb5f21c459b9cf7456d47646906ff%2Fimage3.jpg?alt=media)
3. 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.\
   ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-e7117276465a73c11d3d40b0a7a2118f5882ac8a%2Fimage4.jpg?alt=media)
4. 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.
5. Click Next to Finish.
6. Re-analyze the sample by clicking the "BlueFuse" button on the left.\
   ![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-15f83ce10fc3f13bdfe69d72f67bc8bfc62dd12f%2Fimage5.png?alt=media)

For additional information, see [BlueFuse Multi v4.5 Software Guide](https://support.illumina.com/downloads/bluefuse-multi-software-reference-guide-15053620.html).

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #3859), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000003859%20-%20Microarray%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |