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Hi Russ,
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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">From:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">russ port <<a href="mailto:russgport@gmail.com" class="">russgport@gmail.com</a>><br class="">
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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">Subject:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><b class="">[FieldTrip] 2 (between subject) x 2 (between subject) x 3 (within subject) ANOVA for Time Frequency Plots</b><br class="">
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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">Date:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">22 Jun 2015 17:37:07 CEST<br class="">
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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">Reply-To:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>><br class="">
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Hi All,
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<div style="text-align: justify; widows: 1;" class="">After reading the wiki (<a href="http://www.fieldtriptoolbox.org/faq/how_can_i_test_an_interaction_effect_using_cluster-based_permutation_tests" class="">http://www.fieldtriptoolbox.org/faq/how_can_i_test_an_interaction_effect_using_cluster-based_permutation_tests</a>),
it appears that I cannot do a cluster based permutation test on a set of data I have because of the fact that I have two between subject factors (genotype and sex). There has been a lot of discussion on the mailing list about how to run these kinds of analyses,
but they have always (or at least what I could find), been about data set containing only 1 between subjects factor. As such, I have a question in two parts A) could I look at the data with a proper test of the between subject factors, and the within subject
factor AND their interaction <b class="">using a permutation test that use holms or bonferroni correction</b> (though I would probably use holms because of bonferroni being to conservative) B)
<b class="">should I set this up by either i) testing geno, sex and their interaction separately like I think the wiki suggests above or ii) try and use the </b><span style="text-align: justify; white-space: pre-wrap; widows: 1; background-color: rgb(247, 249, 250);" class=""><b class="">cfg.cvar
input as previously suggested else where on this discussion list</b> (though again that was for data with only 1 between subject
</span><span style="white-space: pre-wrap;" class="">variable)?</span></div>
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<div>With respect to question A: </div>
<div>I hope I understand you correctly here: you want to analyse a 2 (between) x 3 (within) design, separately for the the data selected according to the level of the other between-subjects factor (thus, 2 analyses of a 2x3 design). Yes, this is possible in
the permutation framework. Using Bonferroni correction to account for the fact that you perform 2 tests instead of 1 is a good idea.</div>
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<div>With respect to question B:</div>
<div>You cannot test the interaction geno x sex in the permutation framework because these are 2 between-subjects factors. Also, the cfg.cvar option is to be used in a within-subjects design (or a matched-pairs design, which is statistically equivalent to a
within-subjects design). Thus, the cvar must be within-subjects variable.</div>
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<div>best,</div>
<div>Eric Maris</div>
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<div style="text-align: justify; widows: 1;" class=""><span style="white-space: pre-wrap;" class="">Best,</span></div>
<div style="text-align: justify; widows: 1;" class=""><span style="white-space: pre-wrap;" class="">Russ Port</span></div>
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