Peak Ratio Bar Analysis

Overview

Generates a bar plot image from peak molarity ratio data, one image per primer pair. The bar plot is viewable at the primer pair page with the electropherogram graphs. They are also grouped by gene and are accessible from the gene page. A complete list for all primer pairs is accessible from the main page, but please note that, depending on the number of reactions, this page may take some time to load and may possibly be interrupted by the server timeout. If you need a full list and fail to view it online here, please contact us (see below).

Background

This analysis is a high-level graphical representation of the peak molarity ratio data obtained by the peak ratio data analysis. The molarity ratios for the reaction set of a primer pair are plotted in a horizontal histogram. Peak ratios for a reaction are juxtaposed on the same bar, thus each full bar represents the total molarity for the reaction. Peaks are color-coded by their amplicon length, as shown in the legend below.

Interpretation

Here is an annotated peak ratio bar image for four reactions with the primer pair Abca13.F1 Abca13.R1:

1. primer pair name (name of the forward and reverse primers).
2. Ratios bar. Each reaction is represented by juxtaposed horizontal histogram bars, one per peak. Peaks are coloured differently by their amplicon length. The full bar represents the reaction's total molarity. Thus, each peak can be mapped to an approximate ratio value by evaluating the fraction of the complete bar covered.
3. Sample name for this reaction.
4. Total molarity value for this reaction (nM). This is the molarity sum of all peaks identified in the reaction.
5. Peak legend. Each peaks is assigned a color according to its amplicon length.
6. Dubious peak matching. When a horizontal bar is split with many different colors, this means that those peaks were all assigned to the same detected peak in the peak matching analysis previously run, thus they all share the same molarity ratio. Here the two peaks at 188 bps (red) and 200 bps (green) share the same molarity ratio of 0.3, whereas they are separated and matched to different peaks in the three other reactions.
7. Unexpected peak. The cross-hatched pattern is used to identify an unexpected peak. Here the unexpected peak at 280 bps (blue) is detected in three reactions, but was not detected in the other reaction (brain, treated).

Algorithm

The peak molarity ratio data is directly obtained from the previously run peak ratio data analysis. Peak ratios are bar-plotted for each reaction.

Contacts

• Philippe Thibault

Credits

Philippe Thibault

Implementation of the analysis