We propose a new method of analysis for the \lya forest, namely to measure the 1-point and 2-point joint probability distribution of the transmitted flux. The results for a sample of seven observed quasars and from two simulations of structure formation are shown and compared. Statistically significant differences in the 2-point function between the results of the numerical simulations and the observations are easily found. The analysis we suggest is very simple to apply to observed data sets, and we discuss its superiority over the traditional Voigt-profile fitting algorithms for accurate comparison to the predictions of theoretical models.