Some links that may be helpful: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis http://surfer.nmr.mgh.harvard.edu/fswiki/MultipleComparisons
Hope it helps. PPJ ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom On Tue, Mar 24, 2009 at 12:38, Lars M. Rimol <lari...@gmail.com> wrote: > Hi, > I have done an analysis involving three groups, so there are three pairwise > comparisons across two hemispheres = 6 p-maps. I want to adjust for multiple > comparisons (across the vertices), so I use FDR. But since FDR determines > the threshold basd on the actual p-values, I get 6 different tresholds: > > comparison 1: lh and rh, 0.016 and 0.028 (I can choose .01) > comparison 2: lh and rh, 0.01 and 0.001 (I can choose.001) > comparison 3 lh and rh, 0.001 and 0.0001 (I can choose .0001) > > There are lots of significant vertices in comparison 1 and nothing > significant, after correction, in comparison 3. Is there anything wrong with > using different tresholds here, and concluding that in comparison 1 there > were extensive differences between the groups, whereas in comparison 3 there > were none? I'm not sure if this is a problem, but I'm afraid some reviewers > might have an issue with it. Across the hemispheres, I can choose a > conservative threshold which covers both hemispheres, i.e. lower than both > the FDR-adjusted treshold for lh and rh. But between the comparisons the > tresholds differ even more, by a factor of 10 and 100. And if I choose the > most conservative of all the adjusted thresholds, I'm afraid that I'll make > a type II error in comparison 1. > > From what I understand, the adjusted threshold for comparison 3 is more > conservative because of the actual empirical data (the distribution of > p-values), so that's an empirical argument for using a more conservative > threshold there. > > > And: What if I pooled all thre p-maps (sig.mgh) and did an FDR on the whole > thing, would that be a better approach? And does Freesurfer use the > Benjamini algorithm, and if you do, can I use Tom Nichols' matlab function > for FDR (http://www.sph.umich.edu/~nichols/FDR/FDR.m) for pooling all > three p-maps? > > Thank you! > > -- > yours, > LMR > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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