Fig. 1. Inconsistencies in standard PPI_ratio measurement.

a PPI_ratio from the first Fmr1 cohort of male rats. Blue: WT (n = 7) and red: Fmr1 KO (n = 9) across different prepulse sounds with a constant 100 ms delay and startle sounds of 30 dB above background (top) or 50 dB above background (bottom). b PPI_ratio from the second Fmr1 cohort of male rats. Blue: WT (n = 9) and red: Fmr1 KO (n = 9) across different delays with a constant prepulse of 14 dB above background and startle sounds of 35 dB above background (top) or 50 dB above background (bottom). For a and b, significant group differences, indicated by an asterisk, were defined as a two-way ANOVA with p < 0.05. See Supplementary Methods for further PPI_ratio analysis on these data. c Example probability distribution of gain-normalized movement (see Fig. S2) (left) and log₁₀ of gain-normalized movement (right) for one rat to a startle sound of 40 dB above background with no prepulse. Solid curves are Gaussian functions with mean and standard deviation equal to those of the data and height equal to the height of the bin containing the mean. d Distribution of the differences in log-likelihood of the movement data under a log-normal distribution and the log-likelihood of the movement data under a Gaussian distribution across all rats and stimuli. Positive value indicates that the log-normal distribution had a larger log-likelihood. e Distribution of the Shapiro–Wilks normality test p values across all rats and stimuli for the data before log transformation (light gray) and after log transformation (dark gray). Dotted vertical line shows p = 0.05. Smaller p values indicate greater probability of rejecting the null hypothesis that the data is drawn from a Gaussian distribution. f PPI_ratio using log-transformed movement data for one rat (same rat as Fig. 1c) across five different startle sound levels (x-axis), three different prepulse sounds (colors), and a constant 100 ms delay. Bars show the standard error of the mean. Dotted lines show linear regressions for each prepulse sound level. g Distribution of linear regression slopes of PPI_ratio versus startle sound level (dotted lines in Fig. 1f) across all rats and stimuli. Dotted line shows slope of 0.