[Eeglablist] Help with LIMO ANCOVA/Regression and STUDY cluster analysis

Dr Cyril, Pernet wamcyril at gmail.com
Mon Feb 8 01:30:13 PST 2021

Hi Deniz

> */Thank you very much for your clarifications. This is very helpful. 
> Just a few follow questions:/*
>> the 'best' thing to do would be to compute contrasts, i.e. [1 -1 0] 
>> for each subject which is your main effect, then ANCOVA 2 gp and 
>> covariates
> /*-When I run the first level analysis it only creates 2 beta files, 
> one for each group, but there are not any con files created 
> automatically.*/
> /*Here do you mean, following the first level analysis, I should 
> create contrast files using contrast manager, separately for each 
> independent group, using one-sample t-test and then use these con 
> files in ANCOVA (define contrast [1 -1 0], then run Contrast Manager—> 
> LIMO files for the group —> contrast.mat file —> second 
> level—>one-sample t-test?)*/

we cannot infer what users want to do and the number of (simple) 
contrasts is the binomial coef. of the design matrix rank: N!/K!(N-K)! 
nchoosek in matlab with N the number of regressors and K from 2 to N 
which is why this is not automatic (with a 2*2 design, ie 4 conditions 
that already 11 contrasts but most would be irrelevant)

you can however automatize this easily: 1st create and save a contrast 
file as txt or mat (here simply 1 -1 0),  call limo_batch in the command 
window, choose contrast only, select the list of LIMO files (txt) 
created by study, select that contrast file -- all subjects will be 
processed ; now you can use those con files in the ANCOVA as explained 

> /*
> */
> /*-From what I understand, if I wanted to test the relation between my 
> covariate and  each condition (for each different repeated measure), 
> then I have to create different study designs for each condition (one 
> condition x 2 groups) since I can not include repeated measure in ANCOVA?
> */

that was not what you asked last time ... if you want to check in 
general relationships between variables and covariates use the 2nd level 
regression and there you can enter as many things as you want ; your 1st 
level design remains unchanged

>>> 2)Regression-LIMO
>>> I also thought that if ANCOVA did not work, I could run a regression 
>>> model separately for each independent group.
>>> In the tutorial it gives an example of creating a first level 
>>> contrast for each subject, and then run a-sample t-test to create 
>>> the con files which would be used in the regression model along with 
>>> the regressor variable. I was wondering if there is a way to use 
>>> parameters from the repeated measure ANOVA model as they would 
>>> account for the noise better, or maybe it would not differ much 
>>> since I used OLS?
>> well see above -- if you split the ANCOVA covariates (ie use 
>> XXXXXX000000 and 00000XXXXX with values) say for age, then you 
>> model separately the effect of age for each group - which allws you 
>> to test [1 -1] if group differ, [0 0 1 -1] if the effect of age 
>> differ, [0 0 1 1] the common effect of age
> /*-Here are you referring to post-hoc contrast analysis following 
> ANCOVA? So for the covariate file should I have 2 columns (000XXX  and 
> XXX000) with each column representing values from from one group?
> */

yes make two columns for age, that way you can assess the difference in 
the effect of age between groups (after controlling for overall group 
difference). Now conceptually, if you were to set up a regression, the 
group variables would not be present, and a similar post-hoc contrast 
would also tell you the difference in the effect of age between groups- 
but without controlling for a possible overall group difference (hence 
better here to use ANCOVA)

> /*
> */
> /*Sorry for all the questions, I just wanted to make sure I am doing 
> the right thing! We are getting some excited results with LIMO, so I 
> really hope to be able to finalize my analysis using LIMO, but  at the 
> same time I want to be  confident about the stats and what they mean 
> for when it gets published!*/

you are welcome - Arnaud, Ramon and I work hard to get a nice 
integration but it's only as more people use it we can improve

best wishes


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