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Update genomestudio-background.md
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kbeutel committed Feb 22, 2024
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GenomeStudio allows you to visualize and analyze data generated on Illumina array platforms. You may need to recluster data or do other tasks in GenomeStudio to prepare raw data files that are appropriately formatted for for use in Genvisis.

Illumina Beadchip technology uses a probe 50 base pairs in length and assesses the variant after the fiftieth base pair. AT nucleotides are tagged with a red fluorescent dye and GC nucleotides with green. Samples are fluoresced and the light intensity is measured. Measurements are plotted such that the x-axis is a measure of red intensity, and a pure red signal is labeled the A probe. The y-axis measures green intensity and is called the B probe. Measurements in the middle of the graph cluster as a yellow mixture. Twelve samples per chip can be run at a time.
Illumina BeadChip technology uses a probe 50 base pairs in length and assesses the variant after the fiftieth base pair. AT nucleotides are tagged with a red fluorescent dye and GC nucleotides with green. Samples are fluoresced and the light intensity is measured. Measurements are plotted such that the x axis is a measure of red intensity, and a pure red signal is labeled the A probe. The y axis measures green intensity and is called the B probe. Measurements in the middle of the graph cluster as a yellow mixture. Twelve samples per chip can be run at a time.

The SNP Graph in GenomeStudio represents the x and y light intensity values transformed to R and Theta, where R is the total intensity (i.e., x + y) and theta is the angle of a value on the x-axis. The three clusters on the SNP Graph are the AA, AB, and BB alleles for the SNP. The R-value divided by the centroid of a data cluster is a normalized value called Log R Ratio, which can be mapped in [Trailer Plot](../#/documentation/VisualizeWorkflowResults--trailer-plot).
The SNP Graph in GenomeStudio represents the x and y light intensity values transformed to R and Theta, where R is the total intensity (i.e., x + y) and theta is the angle of a value on the x axis. The three clusters on the SNP Graph are the AA, AB, and BB alleles for the SNP. The R-value divided by the centroid of a data cluster is a normalized value called Log R Ratio, which can be mapped in [Trailer Plot](../#/documentation/VisualizeWorkflowResults--trailer-plot).

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