How can I make a Bland-Altman plot with GraphPad Prism? How can I add dotted lines showing the limits of agreement?

A Bland-Altman plot, also known as a "difference" plot or "method-comparison" plot, is used to compare two assay methods. You measure a bunch of samples using both assays, and plot each sample as a single point. The graph is constructed so the difference between the two measurements (Y axis) is plotted against the average of the two measurements (X axis). 

A Bland-Altman plots compare two assay methods. It plots the difference between the two measurements on the Y axis, and the average of the two measurements on the X axis.

1. Enter the data

Create a new table. Choose the one-way tab and a before-after graph. If you don't have data yet, choose the Bland-Altman sample data.

Enter the measurements from the first method into column A and for the other method into column B. Each row represents one sample or one subject.

2. Choose the Bland-Altman analysis

From the data table, click on the toolbar, and then choose Bland-Altman from the list of one-way analyses.

Designate the columns with the data (usually A and B), and choose how to plot the data. You can plot the difference, the ratio, or the percent difference. If the difference between methods is consistent, regardless of the average value, you'll probably want to plot the difference. If the difference gets larger as the average gets larger, it can make more sense to plot the ratio or the percent difference.

3. Inspect the results

The Bland-Altman analysis creates two pages of results. The first page shows the difference and average values, and is used to create the plot. The second results page shows the bias, or the average of the differences, and the 95% limits of agreement.

If you used the sample data, the two methods have very similar results on average, and the bias (difference between the means) is only 0.24. The 95% limits of agreement are between -13.4 and 13.9.

4. Plot the Bland-Altman graph

The 95% confidence limits of the bias are shown as two dotted lines. They are created using Additional ticks and grid lines on the Format axes dialog. The position of each line was 'hooked' to an analysis constant created by the Bland-Altman analysis.