GraphPad Statistics Guide

Table of means or predicted means

Table of means or predicted means

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Table of means or predicted means

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Starting with Prism 8, Prism can report a table of means as part of two-way ANOVA. Choose to create this table in the Options tab of the two-way ANOVA dialog.

If there are no missing values

If the data are balanced (no missing values) you'll see the label "Means" at the top of this table which shows the cell means, the row means, the  column means, and the grand mean. You'll get the same means for ordinary or repeated measures ANOVA, and could easily compute the values yourself.

If there are any missing values

If the data are unbalanced (there are any missing values), this table is labeled "Predicted means (LS Means)"  for the cell, row, column and grand means. These predicted means, also known as "LSmeans", may not match the ones you compute by hand.

If you have repeated measures and missing values, the situation is complicated. Think about it this way. Prism fits a mixed model to your data, and that model is used to predict the cell means. If there are no missing values, those predictions always equal the actual means of the data. But if there are missing values, the predictions take into account the pattern of missing values, and the experimental design (repeated measures), so the predicted means do not equal the actual means and cannot easily be compute by hand.

Cell, row, column and grand SD

Prism also reports the SD of each cell, which is straightforward. It also reports the SD for each row and column, and SD for the whole table (the grand SD). These are computed by first averaging the replicates in each cell and then computing the SD of those cell means.  If a row has three data set columns, each with five subcolumns for replicates, the n for computing the SD is 3, not 15.