GraphPad Curve Fitting Guide

Residual plot

Residual plot

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Residual plot

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What are residuals?

Unweighted fits

A residual is the distance of a point from the curve. Least-squares regression works to minimize the sum of the squares of these residuals.  A residual is positive when the point is above the curve, and is negative when the point is below the curve. Create a residual plot to see how well your data follow the model you selected. Mild deviations of data from a model are often easier to spot on a residual plot than on the plot of data with curve.

Weighted fits

If you choose to weight your data unequally, Prism adjusts the definition of the residuals accordingly.

The residual that Prism tabulates and plots equals the residual defined in the prior paragraph, divided by the weighting factor.  The most common common alternative weighting is "Weight by 1/Y2 (minimize relative distances squared)". In this case, the residual is defined to be the distance of the point from the curve divided by the Y value of the curve. Weighted nonlinear regression minimizes the sum of the square of these residuals. Note the ambiguity in defining weighting. The Prism dialog gives the choice to weight by 1/Y2. This means that the squared residual is divided by Y2. The weighted residual is defined as the residual divided by Y. Weighted nonlinear regression minimizes the sum of the squares of these weighted residuals.

Earlier versions of Prism (up to Prism 4) always plotted basic unweighted residuals, even if you chose to weight the points unequally.

Which kind of residual graph?

Starting with Prism 8, choose among four kinds of residual plots:


X axis

Y axis

Residual vs. X plot

X values of data

Residual or weighted residual

Residual vs. Y plot

Predicted Y value

Residual or weighted residual

Homoscedasticity plot

Predicted Y value

Absolute value of residual or weighted residual

QQ plot

Actual residual

Predicted residual if residuals are sampled from a Gaussian distribution

Prism only lets you create one residual graph from nonlinear regression. If you want to make two or more kinds of residual graphs, you'll need to duplicate the results page, and then change the residual option on the new copy.

Examples

Example fit

Here is a log(dose) vs. response curve with simulated data. The random scatter was chosen so the points iwth larger Y values have larger average scatter. The fit was done the usual way without weighting. If you look carefully, you can see that the points at the top of the curve have more scatter, but it isn't so obvious.

Residual vs. X

This is the most common residual graph. Prism 7 and earlier only created this kind of residual plot. You can see that the points with large X values have larger residuals (positive and negative).

 

Residual vs. predicted Y

For each point, Prism calculates the Y value of the curve at that X value, and plots that Y value on the X axis of the residual plot. The Y axis of the residual plot graphs the residuals or weighted residuals. You can see that the points with larger Y values have larger residuals, positive and negative.

In this example the Y values get larger as X values get larger. So this graph doesn't look very different than the residual vs. X plot. But if the curve is biphasic, the two graphs will look more different.

Homoscedasticity plot

This graph is made just like the graph of predicted Y vs. residuals, except here the absolute values of the residuals are shown. Now it is really clear that the residuals get larger as Y gets larger.

QQ plot

The X axis plots the actual residual or weighted residuals. The Y axis plots the predicted residual (or weighted residual) assuming sampling from a Gaussian distribution. An assumption of regression is that the residuals are sampled from a Gaussian distribution, and this plot lets you assess that assumption. If the assumption is true, the points should all be very close to the line of identity, shown in red on the graph. QQ plots sometimes plots one or both axes as percentiles are quantiles (same as percentiles but as fractions rather than percentages). Prism always plots both axes in the same units as the Y values of the data.

In this example, the data don't follow the line of identity very well. The data are sampled from Gaussian distributions, but the SD of that distribution was larger when the Y values were larger. The residuals were not sampled from a single Gaussian distribution, and this accounts for the systematic discrepancy between the points and the line of identity.

Same example fit with weighted regression

The data were then fit to the same model but with relative weighting. Here are the four residual graphs. All show that the data now comply with the assumption of the fit.