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David Groppe (view profile)


19 Dec 2010 (Updated )

One sample/paired samples permutation t-test with correction for multiple comparisons

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     Permutation test of the null hypothesis that a set of data was sampled from a symmetric distribution with a particular mean. The test is based on a t-statistic and can be applied to situations in which a one sample or paired sample/repeated measures t-test is appropriate. Note, that this test is more general than parametric t-tests in that it does not assume that the data were sampled from a Gaussian distribution.
     This function can perform the test on one variable or simultaneously on multiple variables. When applying the test to multiple variables, the "tmax" method is used for adjusting the p-values of each variable for multiple comparisons (Blair & Karniski, 1993). Like Bonferroni correction, this method adjusts p-values in a way that controls the family-wise error rate. However, the permutation method will be more powerful than Bonferroni correction when different variables in the test are correlated.
Blair, R.C. & Karniski, W. (1993) An alternative method for significance testing of waveform difference potentials. Psychophysiology.

MATLAB release MATLAB 7.8 (R2009a)
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Comments and Ratings (8)
15 Sep 2015 peggy

peggy (view profile)

25 Jun 2015 David Groppe

David Groppe (view profile)

Thanks for the comment, Kielan. I hadn't realized that de2bi.m had been discontinued by Mathworks. I just uploaded a revised version of the function that should work.

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30 Apr 2015 Kielan

Kielan (view profile)

Nice file, but I think there is a bug in the exact test part (for N <= 12) which didn't appear to be testing all possible permutations. Possible fix copied next:

if exact,
%Use all possible permutations

for i = 1:n_obs
sets{i} = [-1 1];

c = cell(1, numel(sets));
[c{:}] = ndgrid( sets{:} );
AllPerms = cell2mat( cellfun(@(v)v(:), c, 'UniformOutput',false) )';


for perm=1:n_perm
if ~rem(perm,100)
if reports,
if ~rem(perm-100,1000)
fprintf(', %d',perm);
if ~rem(perm,1000)
%set sign of each participant's data


% if exist('de2bi.m','file') %% ?? check
% temp=de2bi(perm-1);
% else %% check ??
% temp=perm-1; %% check ??
% end %% check ??
% n_temp=length(temp);
% sn=-ones(n_obs,1);
% sn(1:n_temp,1)=2*temp-1;

sn = AllPerms(:,perm);


%computes t-score of permuted data across all channels and time points

%get most extreme t-score
[dummy mxt_id]=max(abs(t));
mxt(perm)=t(mxt_id); %get the most extreme t-value with its sign (+ or -)

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18 Jul 2014 Pierre M├ęgevand  
15 Apr 2014 Joana Paiva


I would like to know if anyone knows if it possible to perform a repeated measures ANOVA (more than 2 conditions per subject) using your function 'mult_comp_perm_t1' and how I can do that. In the function's description it says that:

Paired-Sample/Repated Measures Example:
% >> dataA=randn(16,5); %data from Condition A (5 variables, 16 observations)
% >> dataA(:,1:2)=dataA(:,1:2)+1; %mean of first two variables is 1
% >> dataB=randn(16,5); %data from Condition B (all variables have mean of 0)
% >> dif=dataA-dataB; %difference between conditions
% >> [pval, t_orig, crit_t, est_alpha, seed_state]=mult_comp_perm_t1(dif,50000);
% >> disp(pval); %adjusted p-values

But it refers to Repeated Measures ANOVA? The example only considers two conditions... for computing more than that, can I taking the differences among them (cond1-cond2-cond3-cond4)?

Thank you,

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09 May 2013 Cecile

Cecile (view profile)

I have a question. If est_alpha value is 0 (I have 12 observations). the p-value is still correct (in my case p=0)? Should I use and other test ? change a parameter?
Thanks a lot.

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09 May 2013 Cecile

Cecile (view profile)

very nice..Thanks

22 Apr 2011 Jiachen Zhuo

Nice program. Thank you.

03 Feb 2011 1.1

Karniski reference was misspelled as "Karnisky" and has been fixed. 'alpha_level' input option and 'crit_t' and 'est_alpha' output options added.

17 Sep 2012 1.2

Comments updated.

25 Jun 2015 1.3

Function no longer requires de2bi.m, which apparently has been discontinued. Lack of this function would produce errors when # of obs was <=12. Thanks Kielan!

01 Jul 2015 1.3

Command line output cleaned up.

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