Methods of site‐response analysis require theoretical and empirical testing and validation before they can be used in seismic‐hazard assessment. Comparison of site amplification functions (SAFs) calculated using earthquake data recorded by seismic arrays with SAF obtained using analytical approaches represent the most important tests of reliability of those methods. High‐quality, low‐amplitude earthquake data recorded by the Treasure Island (TI) downhole array between 1993 and 2010 were used for comparisons with the two versions of the equivalent linear (EQL) site‐response methods implemented in the computer program STRATA (Kottke and Rathje, 2008; Rathje and Kottke, 2013): Use of the TS approach in STRATA matches well the empirically determined SAF between the bedrock and the surface. The STRATA version of the RVT approach can produce a significantly different SAF from the empirically determined and the TS approach. Further testing of different realizations of the RVT method is desirable to assess the method’s reliability and limitations. The paper of Kottke and Rathje (2013) raises a very important issue of comparison of the two site‐response analysis approaches: classical TS SHAKE‐type (Idriss and Seed, 1968; Idriss and Sun, 1992) and RVT (Vanmarcke, 1975; Der Kiureghian, 1980; Hanks and McGuire, 1981). These approaches represent two versions of EQL site‐response analyses. I found this discussion timely, because more and more probabilistic seismic‐hazard projects, including those for critical facilities, use the RVT approach. Kottke and Rathje (2013) properly pointed out that the fact that the RVT site‐response analysis does not require input TS makes it an attractive alternative to the TS approach. Nevertheless, the main questions are: