Regardless: FDR's sensitivity appears resolution-dependent to me.
On 10/16/2009 10:39 AM, Michael Harms wrote:
Interesting post Donna, but my understanding of FDR is that it sets the p-value threshold based on the LARGEST p-value that satisfies the FDR relationship.
That is, steps 3 and 4 in Genovese et al. (2002) are: 3) Let r be the largest i for which p <= i/V*q (assuming c=1) 4) Threshold the image at the p-value p(r).
So, it isn't the case that you require the most significant p-value to satisfy p <= 0.05/V "just to get past i=1" as you put it in your post.
Rather, you pick the largest p-value that satisfies the relationship, meaning that lower (more-significant) p-values may not have necessarily satisfied p <= i/V*q for their particular position in the sorted list of p-values.
cheers, Mike H.
On Fri, 2009-10-16 at 10:13 -0500, Donna Dierker wrote:
I never heard anything on my post here, but it might just be high surface resolution:
http://www.mail-archive.com/neuro-mult-comp@brainvis.wustl.edu/msg00026.html
On 10/16/2009 09:58 AM, Michael Harms wrote:
Your FDR analysis sounds correct. You probably have a rather small number of "marginally" significant vertices, which is why none survive FDR. You could try increasing the "q" value from say 0.05 to 0.1, in which case 10% of the surviving vertices would be expected to be false positives.
cheers, Mike H.
On Fri, 2009-10-16 at 12:03 +0200, Yulia WORBE wrote:
Dear Freesurfer team,
We are currently doing a cortical thickness studies between a group of psychiatric patients (n=60) and controls (n=30). We tested several smoothing levels (15mm, 20mm, 25mm)
When setting an uncorrected threshold (such as p<0.005), we obtained several regions of decreased thickness, which are consistent with the pathology.
However, when trying to correct for multiple comparisons using FDR ("Set Using FDR" button in qdec), the computed threshold is very high (e.g. 4.3 for 20mm smoothing) and, obviously, no significant regions are left.
Did we do anything wrong in the analysis ?
Thank you very much for your help, Yulia
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