Interpreting Microarray Data: Converting Light Intensities to Numbers

Before data can be analyzed, the different colors of the dots have to be converted to numbers. There are many approaches, but here we show a simplified version of a common technique. Let us consider a simple case involving only four genes.

First, each spot is converted to a number that represents the intensity of red dye and green dye. In this example, we use arbitrary light units.

Next, we calculate the ratio of red to green (red ÷ green).

Red (tumor)
light intensity

Four circles of varying shades of red arranged in a square and labeled A, B, C, and D.

Red (tumor) light intensity
Gene A: 400	Gene B: 200
Gene C: 100	Gene D: 400

Green (normal)
light intensity

Four circles of varying shades of green arranged in a square and labeled A, B, C, and D.

Green (normal) light intensity
Gene A: 100	Gene B: 200
Gene C: 300	Gene D: 400

Ratio red/green
(tumor/normal)

Four circles of varying shades of green, red, and yellow arranged in a square and labeled A, B, C, and D.

Ratio red/green (tumor/normal)
Gene A: 4	Gene B: 1
Gene C: 0.33	Gene D: 1