help > RE: NBS: test_stat interpretation with FDR analysis
Jun 18, 2019  12:06 AM | Cecile Bordier
RE: NBS: test_stat interpretation with FDR analysis
Hi,

Sorry I should have given more details. But yes, you comfort what I was thinking about negative values.

So more details. I have a group of 61 subjects with acquisition at 3 time points (6months, 36months and 60months respectively M6, M36 and M60).

So I use the fsl (feat) website to create my design matrix. Here is an example for 2 subjects:

 1  1 1 0
 1  1 0 1
-1  0 1 0
-1  0 0 1
 0 -1 1 0
 0 -1 0 1

With the two first columns coding the timepoints and the 2 last for the subjects
So one of my contrast to get M6-M60 is [1 2 0 0].

Basically,  I ran that design on NBS (with nbs stat, a t-test, 5000 permutations, block exchange 1:61,1:61,1:61 (for my 61 subjects)) and I got stat at 0.054. So close of significance that I decided to try the FDR analysis. I increased the number of permutation to 100000, changed the stat to FDR  (kept the exchange blocks is it right?) and ran it.
It took a long time and I got significant results (for my 3 contrasts M6-M60; M6-M36 and M36-M60).
So my idea to represent them was to multiply nbs.NBS.con_mat with nbs.NBS.test_stat and plot the connection which were not equal to zeros. But here I am getting positive and negative values (even low values) and that for the results of my three contrasts.

I think I must do something wrong, but I  have trouble figuring where.
Thanks a lot for your patience and help.

Cecile

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TitleAuthorDate
Cecile Bordier Jun 17, 2019
Andrew Zalesky Jun 17, 2019
RE: NBS: test_stat interpretation with FDR analysis
Cecile Bordier Jun 18, 2019
Andrew Zalesky Jun 18, 2019
Cecile Bordier Jun 19, 2019
Bordier Cecile Jun 24, 2019
Andrew Zalesky Jun 24, 2019
Cecile Bordier Jul 1, 2019