I have preference ratings (1-to-7 scale) for k=80 stimuli, obtained from N=30 subjects. I would like to do a multiple regression for these scores, against a small number of weakly-correlated predictors. Some of the predictors are continuous, others are categorical. Also, some of the predictors characterise the subject (e.g. age), while others characterise the stimulus (e.g. loudness).

I am confused whether the regression should take in cross-stimulus or cross-subject variability. I will be using the 'regress' function in Matlab:

b = regress(y,X) returns a p-by-1 vector b of coefficient estimates for a multilinear regression of the responses in y on the predictors in X. X is an n-by-p matrix of p predictors at each of n observations. y is an n-by-1 vector of observed responses.

I know the regression line is normally fit between data points that represent different subjects, not different stimuli (repeated measures). In this assumption, the Y matrix (i.e. the different observations) would contain all subjects' scores for a single stimulus. But this would mean I have to do k multiple regressions (one for each stimulus), which seems to me like a mass-univariate apporach, whereas I'd have thought this is a multivariate problem.

My questions are:

1) How should the ratings for the different subjects, and for the different stimuli, be arranged to define the Y and X matrices in the regression formula?

2) Do I need to do a separate regression for each stimulus, and if so, is a multiple comparisons correction necessary?

3) Should multiple regression not in fact be the most optimal tool in this case (e.g. due to the rather low sample size), would mixed-effects modelling be more suitable? If so, the same questions regarding how the cross-subject vs cross-stimulus variability should be arranged in the input and output matrices.


1 Answer 1


The most obvious approach here is indeed a single mixed model for all the data. Each subject–stimulus pair should get a row in $X$ and a value in $y$, so you'll have $30 \cdot 80 = 2,400$ cases. You can then include a random intercept for each stimulus and a random intercept for each subject. A vignette for the R package lme4, "Fitting Linear Mixed-Effects Models using lme4", says "Such models are common in item response theory, where subject and item factors are fully crossed." (p. 7)

  • $\begingroup$ Thanks. Am struggling to define this, though. Namely: 1) you suggest to have 30*80=2400 rows in the table array expected by fitlme, but that would mean a lot of repetition of both stimulus- and subject-specific predictors! 2) how to define the mixed-model formula using the Wilkinson notation that the fitlme function expects 3) which of fitlme's many outputs to report, e.g. is one fit statistic per regressor enough?! $\endgroup$
    – z8080
    Commented Nov 8, 2016 at 15:36
  • 1
    $\begingroup$ I can't speak for MATLAB (I haven't used its statistics routines). "that would mean a lot of repetition of both stimulus- and subject-specific predictors" — Yes. This is not a problem. What potentially would be a problem is the dependencies between different items for the same subject and different subjects for the same item, but the point of using a mixed model is to include random effects to account for these dependencies. "which of fitlme's many outputs to report" — It depends on what you ultimately want to do with the model. Try reading some introductory material on mixed models. $\endgroup$ Commented Nov 8, 2016 at 17:22

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.