Who says FDR is more conservative? It all depends on the thresholds you choose.
Note that the FDR threshold is different from the cluster-based p
threshold, and it isn't necessarily appropriate to use the same for
both.
The cluster-based p threshold controls the overall probability that you will
get 1 or more false positives. With p<0.05, the idea is that if you repeated
your study 20 times, 19 times out of 20, you would have NO false positives.
With an FDR threshold of 0.05, you are guaranteed that 5% of your
"significant" vertices are false positives. A more conservative
threshold would be 0.01.
By the way, for cluster thresholding, there are two p thresholds that are
important. The first is the p threshold applied to the z-stats or t-stats
before finding clusters. 0.05 would usually be too liberal. 0.01 or 0.001
would be better. The second is the multiple comparison corrected p value, for
which you would usually use 0.05.
Date: Fri, 29 Jan 2010 10:02:45 -0500
From: stefan.bra...@googlemail.com
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] thickness maps: FDR versus Monte Carlo - different
results
Hi there,
we are struggling with one question and haven't yet heard back. We would be
very grateful for any advice or recommendation.
We were running an analysis (95 subjects) examining a group effect (two groups,
controlling for the effects of a covariate and two cofactors, DODS model) on
cortical thickness with mri_glmfit. We then corrected our results for multiple
comparisons using two methods, FDR and Monte Carlo simulation with 4000
repeats. The threshold was set at p=0.05 respectively. Although examining the
same population we got results in very different regions.
command for the simulation:
mri_glmfit-sim --glmdir xxxx.glmdir --sim mc-z 4000 1.301 mc-z abs.1.301
--sim-sign abs
the fdr results were obtained setting the fdr-threshold at p=0.05 with the
tksurfer script command (sclv_set current_threshold_using_fdr 0.05 0)
With the fdr method we found a spot in the left supramarginal gyrus and with
the clusterwise correction we got a cluster in the right middle temporal lobe
(see pictures of corrected and uncorrected results attached). No other
clusters/findings survived one of the correction methods.
We are well aware of the fact that FDR and Monte Carlo simulation are very
different statistical methods and that FDR is more conservative. Does that
explain the discrepant results? Would you expect a highly robust FDR finding to
not show up at all when using Monte Carlo? What additional information could be
used to decide which method to use for the final models?
Thank you,
Stefan
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