When you choose the False Discovery Rate (FDR) approach to multiple comparisons after ANOVA, Prism does the following:

1.Perform the comparisons you requested using the unprotected Fisher's LSD test. This results in a P value for each comparison. These P values do not correct for multiple comparisons. They are not multiplicity adjusted P values.

2.Use the FDR approach you chose (Prism offers three variants) to decide which P values are small enough to be deemed "discoveries". This calculation depends on which method you chose, and the value of Q you chose (the desired false discovery rate, as a percentage).

3.For each comparison, also compute a q value. The q values will be different for each comparison. If you had set Q to this value (what Prism reported as q) then this comparison would have been right on the border of being a "discovery" or not.

Notes:

•When you choose the FDR approach, Prism will not report anything about statistical significance, and will not (cannot) report confidence intervals or multiplicity adjusted P values. But it does report q values, which are similar to adjusted P values.

•While the FDR approach is often used to deal with many P values such as those computed by Prism's multiple t test analysis, they are not commonly used as followup tests for ANOVA.

•The variable q is used as part of the results of the FDR approach to multiple comparisons, and as part of the Tukey and Dunnett multiple comparisons tests. The three tests define the variable q differently so they should not be compared.