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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Phillipp,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The idea was, that I don’t have to recalculate my statistics if I just want to look at the results with a higher threshold. So, thanks a lot for
your additional information, it helps me to think over my analysis in the first place …<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">thanks, have a nice day!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Iris<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> fieldtrip-bounces@science.ru.nl [mailto:fieldtrip-bounces@science.ru.nl]
<b>On Behalf Of </b>Philipp Ruhnau<br>
<b>Sent:</b> Freitag, 13. November 2015 17:29<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> Re: [FieldTrip] permutation test: multiple comparison correction for the p-values<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hey Iris,<o:p></o:p></p>
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<p class="MsoNormal">you could use matlabs inbuilt function (mafdr) to produce corrected p-values,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">then again if you just want to check your outcome with a higher threshold you might as well feed that into the fieldtrip statistics function with cfg.alpha<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">It is possible to estimate corrected p-values by hand, the logic being the following <o:p></o:p></p>
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<p class="MsoNormal">as in Julian’s example for 5 tests bonferroni adjustment is alpha_level/5. but you could also multiply your p-value with 5 and keep the original threshold.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">similarly for a simple Benjamini-Hochberg fdr if you have a vector with p-values (original_pvals) you do<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Courier"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Courier">pvals = sort(original_pvals);
<span style="color:#25992D">% sort</span><o:p></o:p></span></p>
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<p class="MsoNormal" style="min-height: 13px"><span style="font-size:8.5pt;font-family:Courier;color:#25992D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Courier;color:#25992D">% correct p-vals by hand<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Courier">n = numel(pvals);<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Courier">cor_pvals = pvals .* (n./(1:n));<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier"><o:p> </o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">so following the fdr logic you correct each p-val by its own factor. <o:p></o:p></p>
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<p class="MsoNormal">but note that this is not the fdr correction that is implemented in fieldtrip (see fieldtrips fdr.m for the reference)<o:p></o:p></p>
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<p class="MsoNormal">and that some p-values now can exceed 1…<o:p></o:p></p>
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<p class="MsoNormal">Also I think Arnaud Delorme’s fdr function in eeglab had the option to estimate corrected p-values (but I haven’t checked for quite a while)<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">but yeah, I’m with Julian on this one. as the t-value doesn’t change it certainly makes more sense to quote fdr-corrected p < 0.05 then an exact but corrected p-value<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">hope this helps<o:p></o:p></p>
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<p class="MsoNormal">philipp<o:p></o:p></p>
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<p class="MsoNormal">On 13 Nov 2015, at 16:41, Steinmann, Iris <<a href="mailto:iris.steinmann@med.uni-goettingen.de">iris.steinmann@med.uni-goettingen.de</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Julian,</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks a lot for your advice! But I wane keep all the p-values. Maybe to check what will happen when I would go with a more liberal threshold (maybe
p = 0.06 instead of p = 0.05). So, is there any possibility to correct my p-values directly instead of only the mask?</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Best wishes!</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Iris</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span class="apple-converted-space"><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> </span></span><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""><a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a>
[<a href="mailto:fieldtrip-bounces@science.ru.nl">mailto:fieldtrip-bounces@science.ru.nl</a>]<span class="apple-converted-space"> </span><b>On Behalf Of<span class="apple-converted-space"> </span></b>Julian Keil<br>
<b>Sent:</b><span class="apple-converted-space"> </span>Freitag, 13. November 2015 09:51<br>
<b>To:</b><span class="apple-converted-space"> </span>FieldTrip discussion list<br>
<b>Subject:</b><span class="apple-converted-space"> </span>Re: [FieldTrip] permutation test: multiple comparison correction for the p-values</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Hi Iris,<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">I'm not sure what you want to do with the p-values in the following, but you can multiply your (FDR-corrected) mask with the prob.<o:p></o:p></p>
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<p class="MsoNormal">This would look like this: stat_TF.prob_new = stat_TF.prob .* stat_TF.mask;<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Now you only have the significant p-values left in your prob_new-field, everything else is set to 0.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Hope this helps<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Julian<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif"">********************</span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif"">Dr. Julian Keil</span></b><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif"">AG Multisensorische Integration<br>
Psychiatrische Universitätsklinik<br>
der Charité im St. Hedwig-Krankenhaus<br>
Große Hamburger Straße 5-11, Raum A007<br>
10115 Berlin</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif""><br>
Telefon: +49-30-2311-1879<br>
Fax: +49-30-2311-2209 </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif""><a href="http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration"><span style="color:purple">http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration</span></a></span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Am 13.11.2015 um 09:41 schrieb Steinmann, Iris:<o:p></o:p></p>
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<br>
<br>
<o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Hi everybody,</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">I' m using the 'ft_freqstatistics' function to find significant differences between two time-frequency spectra</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">(see the used options down below).</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">While fieldtrip calculates the permutation test it throws the following information:</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">"performing FDR correction for multiple comparisons</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">the returned probabilities are uncorrected, the thresholded mask is corrected"</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Since I'm using the p-values for the following analysis and not the thresholded mask, I was wondering how I</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">get my p-values corrected for multiple comparison?</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Does anyone has an idea? Thanks in advance!</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">I used the following options:</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg = [];</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.channel = 'all';</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.latency = [2.3 2.8];</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.avgoverchan = 'yes';</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.avgovertime = 'no';</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.frequency = [9 14];</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.parameter = 'powspctrm';</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.alpha = 0.05;</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.tail = 0;</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.correctm = 'fdr';</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.correcttail = 'prob';</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.ivar = 1; </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.statistic = 'ft_statfun_indepsamplesT';</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.method = 'montecarlo'; </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.design = design; % defined in at the beginning of the function</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">cfg.numrandomization = 1000;</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif"">stat_TF = ft_freqstatistics(cfg, TF_remove, TF_noremove)</span><o:p></o:p></p>
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<div>
<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif"">_______________________________________________<br>
fieldtrip mailing list<br>
<a href="mailto:fieldtrip@donders.ru.nl"><span style="color:purple">fieldtrip@donders.ru.nl</span></a><br>
<a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip"><span style="color:purple">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</span></a></span><o:p></o:p></p>
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</div>
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<p class="MsoNormal"> <o:p></o:p></p>
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</div>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Helvetica","sans-serif"">_______________________________________________<br>
fieldtrip mailing list<br>
<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
<a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></span><o:p></o:p></p>
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</blockquote>
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<p class="MsoNormal"><o:p> </o:p></p>
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