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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hey Julian,<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">thanks, you are right! I thought instead of correcting the threshold on which I consider significance, it would be possible to fix the threshold
at 0.05 and adapt the p-values. Maybe that’s really not possible… so, thanks for your comprehensive explanation. I will go with your first advice and multiply the p-values with the mask.<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 a lot and have a nice weekend!<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">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>
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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>Julian Keil<br>
<b>Sent:</b> Freitag, 13. November 2015 17:00<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>
<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">maybe I completely miss your point, could you describe what you want to do with your p-values?<o:p></o:p></p>
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<p class="MsoNormal">Please keep in mind, that a correction for multiple comparisons does not change your p-values, it changes the threshold after which a p-value is significant.<o:p></o:p></p>
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<p class="MsoNormal">Think about the very simple Bonferroni-correction: If you have 5 tests, you set your significance-level to 0.05/5 = 0.01, then compute your 5 t-tests and see which p-value is below 0.01 (instead of below 0.05). This does not affect the
t-tests, or the p-value or t-value of the tests themselves, but only the level you consider significant.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">tl;dr: You don't correct your p-values, you correct the level after which you consider them significant.<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">Am 13.11.2015 um 16:41 schrieb Steinmann, Iris:<o:p></o:p></p>
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<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><span class="apple-converted-space"> </span>[<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";color:black">********************</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";color:black">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";color:black"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif";color:black">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";color:black"><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";color:black"><a href="http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration">http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration</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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<p class="MsoNormal"><br>
<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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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif"">_______________________________________________<br>
fieldtrip mailing list<br>
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<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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<p class="MsoNormal"> <o:p></o:p></p>
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<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">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><o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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