When you use DeCyder™ Differential Analysis Software to calculate spot volumes, how do you normalize the absolute values so that they can be compared from one gel to another?
Spot volumes are normalized within a co-detected image pair in DIA using the blue model histogram that is visible in the graph (see Fig 2). A plot is generated of the number of spots against log (volume ratio) and this should show a normal distribution (red line in Fig 2). As the samples are related, most of the spots will show no change (ratio = 1, log[volume ratio] = 0) so the peak should be centered on 0. The software locates this peak, fits it to a model histogram, and then centers this at zero. Fig 2. Normalization of spots in DIA. In BVA, gel-to-gel spot ratios are compared. Because these ratios are of a sample compared to a common standard, they do not need to be normalized further. The ratio is a relative measurement against a standard. For a more detailed explanation of DeCyder Differential Analysis Software, please refer to the DeCyder Differential Analysis Software User Manual.
Related Questions
- When you use DeCyder™ Differential Analysis Software to calculate spot volumes, how do you normalize the absolute values so that they can be compared from one gel to another?
- Can we choose our own experimental design and still use the DeCyder™ Differential Analysis Software?
- Can we choose our own experimental design and still use DeCyder™ Differential Analysis Software?
