Dear Maxime,
As mentioned in the help text of spm_P_FDR.m, the FDR q-values are
computed using the definition of equation 3 from:
Yekutieli & Benjamini (1999). "Resampling-based false discovery rate
controlling multiple test procedures for correlated test statistics". J
of Statistical Planning and Inference, 82:171-196.
http://dx.doi.org/10.1016/S0378-3758(99)00041-5
Otherwise, draw a line passing through the origin and the uncorrected
p-values of the statistic you want to compute the q-value for, and read
the ordinate of the intersection of this line with the right axis (at
x=1). Depending of the profile of sorted uncorrected p-values, it might
be clearer, at least intuitively, why the ordinate described above might
not increase monotonically with increasing uncorrected p-values. This is
the pendant of the use of find(Ps<=Fi, 1, 'last') in spm_uc_FDR.m to
find the FDR critical threshold.
Maybe it will be simpler if you share the list of uncorrected p-values
(for peaks or clusters so that you don't have too many) that give rise
to the behaviour you describe.
Best regards,
Guillaume.
On 15/12/16 13:47, Maxime Résibois wrote:
> Dear Guillaume,
>
> Thank you very much for your response and for confirming that results are valid.
> I had a look at the slides, they spoke to me as I also read Genovese & al. 2002.
> From what I understand, p-values are sorted and those being below a threshold calculated from P <= i/V * q/c(V) are declared as "active".
> However, it remains unclear to me how those "validated as active sorted p-values" are being assigned a FDR p-value (i.e. how p-values are assigned to green and red dots), and why SPM chooses the minimum value in (min(QS(I:S))?
>
> I would like to also thank you for your script. I used it also for cluster-FDR to see where the cut-off is (when using Ps I had a very smoothed curve with many values that was not very informative), but It did not help responding to the above question.
>
> Kind Regards,
>
--
Guillaume Flandin, PhD
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG
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