Dear All,<br><br>In a study I am trying to test developmental (i.e., age) effect on ERSPs and ERPs. Although I have more than 100 children tested, the number of artifact-free trails for each subject is on average only about 20 and with large variations (ranging from several to several dozens). I can regress these ERSP/ERP measures on age while control for trial number, however, with many subjects having very few trials, the regression analysis may be influenced by those low-trial (consequently, high noise) data points. Covariating the trial number may not solve the problem (if not adding new problems). <br>
<br>After reading a previous discussion among Drs. Delorme, Scott, Rousselete, and Robert (see below), I am thinking whether I can also use a nonparametric statistical analysis: One option is to pool all the trials from all the subjects, then, randomly split the trials into psudo Young and Old trials, and calculate differences on ERSP and ERP measures. Repeat this e.g., 500 times to get null distribution. Then using true age information to split the trials again into true Young and Old trials, and calculate the ERSP/ERP differences again. Finally, I can check whether the real age differences fall within or outside the 95% confidence interval of the null distribution. <br>
<br>The questions are: 1) Because there are 100 subjects, should the results be generalized to the whole population from which I sampled? 2). Now with each ERP/ERSP calculation using about 1000 trials (although the trials are from different subjects), can I believe that the stability of the data can be improved and I may have better chance to detect significant age effect? 3). Will there be a difference (theoretically or in terms of statistical power) if I randomly choose with replacement the psudo Young and Old trials (i.e., bootstrapping the pooled trials) instead of using permutation method?<br>
<br>Based on my limited reading, I did not find relevant literature on this kind use of non-parametric methods. So I would really appreciate if someone can give me some suggestions.<br><br>Have a good holiday!<br><br>Zhongxu<br>
<br><br><br><br><br><div class="gmail_quote">On Wed, Nov 18, 2009 at 6:20 PM, <span dir="ltr"><<a href="mailto:eeglablist-request@sccn.ucsd.edu">eeglablist-request@sccn.ucsd.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Send eeglablist mailing list submissions to<br>
<a href="mailto:eeglablist@sccn.ucsd.edu">eeglablist@sccn.ucsd.edu</a><br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
<a href="http://sccn.ucsd.edu/mailman/listinfo/eeglablist" target="_blank">http://sccn.ucsd.edu/mailman/listinfo/eeglablist</a><br>
or, via email, send a message with subject or body 'help' to<br>
<a href="mailto:eeglablist-request@sccn.ucsd.edu">eeglablist-request@sccn.ucsd.edu</a><br>
<br>
You can reach the person managing the list at<br>
<a href="mailto:eeglablist-owner@sccn.ucsd.edu">eeglablist-owner@sccn.ucsd.edu</a><br>
<br>
When replying, please edit your Subject line so it is more specific<br>
than "Re: Contents of eeglablist digest..."<br>
<br>Today's Topics:<br>
<br>
1. Re: statistics in EEGLAB (Robert Brown)<br>
<br><br>---------- Forwarded message ----------<br>From: Robert Brown <<a href="mailto:bobrobbrown@googlemail.com">bobrobbrown@googlemail.com</a>><br>To: Guillaume Rousselet <<a href="mailto:g.rousselet@psy.gla.ac.uk">g.rousselet@psy.gla.ac.uk</a>>, arno delorme <<a href="mailto:arno@ucsd.edu">arno@ucsd.edu</a>><br>
Date: Wed, 18 Nov 2009 12:39:16 +0200<br>Subject: Re: [Eeglablist] statistics in EEGLAB<br>thank you very much for your responses,<br><br>I'll try to proceed with the strategy proposed by myself and supported by Scott and Guillaume (1. do the single trial analysis in a single subject. 2. look, if and where there is overlap in the effects).<br>
<br>one question remains (just to be sure to be doing the right thing): is the eeglab newtimef function in case of condition comparisons providing me the required "single subject single trial" analysis? (that is, if the alpha-level output is showing me regions where in case of this subject there are significant differences between the conditions as evaluated on basis of single trials. I could not be sure of this, because the alpha level is also computed for the conditions). if not, then can you please lead me to the more appropriate way of doing this in eeglab (I know this is possible in fieldtrip, but I've already done all the other analysis and preprocessing in eeglab).<br>
<br>thank you very much for your time and for your ideas.<br><br>best,<br>Bob<br><br><div class="gmail_quote">2009/11/17 Guillaume Rousselet <span dir="ltr"><<a href="mailto:g.rousselet@psy.gla.ac.uk" target="_blank">g.rousselet@psy.gla.ac.uk</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div>Robert,</div><div><br></div><div>there is no theoretical reason to limit your statistical analyses to group effects. It can be easily argued that you will have actually more power when you do a comparison across 200 trials, rather than across 10 subjects. Chances that a robust effect will occur by chance in 4 subjects are almost null if you have enough trials and a clean signal. So you could do your stats across trials in each subject, show the data for each subject, and then report something like the number of subjects showing a significant effect at any given time point, electrode, or for a given cluster, ICA...</div>
<div><br></div><div>I've been exploring the possibilities of taking into account the variance within observers in the following papers:</div><div><br></div><div><div style="margin: 0px 0px 0px 36px;">Rousselet, G. A., Husk, J. S., Bennett, P. J., & Sekuler, A. B. (2008). <span style="font: 12px Times;">Time course and robustness of ERP object and face differences</span>. <i>Journal of Vision, 8</i>(12), 3, 1-18, <a href="http://journalofvision.org/18/12/13/" target="_blank">http://journalofvision.org/18/12/13/</a>, doi:10.1167/1168.1112.1163.</div>
<div style="margin: 0px 0px 0px 36px;">Rousselet, G. A., Pernet, C. R., Bennett, P. J., & Sekuler, A. B. (2008). Parametric study of EEG sensitivity to phase noise during face processing. <i>BMC Neuroscience, 9:98</i>, <a href="http://www.biomedcentral.com/1471-2202/1479/1498/" target="_blank">http://www.biomedcentral.com/1471-2202/1479/1498/</a>.</div>
<div style="margin: 0px 0px 0px 36px;"><span style="font-size: medium;"><br></span></div></div><div>Best,</div><div><br></div><div>GAR</div><div><div></div><div><div><br></div><div><br></div><div><br></div><br>
<div><div>On 13 Nov 2009, at 18:48, Scott Makeig wrote:</div><br><blockquote type="cite">I agree. For example, if there are 3 subjects, then simple binomial probability can give no better a result than p <= 12.5%. However, in the case that each single-subject effect, across single trials, is significant (e.g., at the p < .001% level), a much stronger inference can be derived using reasonable subject distribution assumptions.<div>
<br></div><div>Scott<br><br><div class="gmail_quote">On Thu, Nov 12, 2009 at 4:03 AM, Robert Brown <span dir="ltr"><<a href="mailto:bobrobbrown@googlemail.com" target="_blank">bobrobbrown@googlemail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> Dear Arno and All,<br><br>thank you very much for your enlightening response. <br><br>maybe one idea: let's say that I only have 4 subjects. the statistics based on "subject means" would be unreliable and I would not get any results. however, it could be that in case of each single subject there is a significant difference based on trials in the same time window, which would actually be a strong evidence for differences between the conditions and which could be written as "in case of each single subject p < .05 (corrected)". I am sorry if this is not right, but I assume that there could be instances where the group statistics with 3-4 subjects would not show anything but the single trial statistics would. (good examples of important studies with so few subjects would be Tong & Engel, 2001 in Nature with 4 subjects fMRI and Resulaj et al., 2009 in Nature with 3 subjects behavior.). <br>
<br>to conclude: maybe the single trial statistics would work, if it a) would be calculated individually for each subject based on only this subjects single trials and then b) the (time-frequency) regions would be plotted, where all the subjects have significant differences based on their single trial analysis.<br>
<br>thank you for your attention and good luck,<div><div></div><div><br>Bob<br><br><div class="gmail_quote">2009/11/11 Arnaud Delorme <span dir="ltr"><<a href="mailto:arno@ucsd.edu" target="_blank">arno@ucsd.edu</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> <div>Dear Bob,<div><br></div><div>thanks for the comments. I think you are using the statmode option "trial" from the command line. This option is quite experimental. It was implemented a while ago and is probably not forward compatible with more recent changes. Also, the "statmode", "trials" option (assuming it was working) should only be used to plot a single subjects. The reason is based on the type of null hypothesis.</div>
<div><br></div><div>When testing with 'statmode', 'subject' for two conditions, the NULL hypothesis is: given the subjects I have recorded and given that these subjects are a good representation of the general population of all possible subjects, there is no difference between the ERP/spectrum/ERSP/ITC between the two experimental conditions in the general subject population. Using parametric, permutation, or bootstrap statistics (and assumptions) you may either accept or reject this hypothesis at a given confidence level.</div>
<div><div><br></div></div><div>When testing with 'statmode', 'trial' on a single subject (still two conditions), the NULL hypothesis is : given the trials I have recorded and given that these trials are a good representation of all the population of trials for this subject, there is no difference between the ERP/spectrum/ERSP/ITC between the two experimental conditions for this subject. Again, using parametric, permutation, or bootstrap statistics (and assumptions) you may either accept or reject this hypothesis at a given confidence level.</div>
<div><div><br></div><div>As you can see the two hypothesis are quite different. One makes an inference about the population of subjects and the other one about the population of trials.</div><div><br></div><div>Now if you pool the trials from different subjects and attempt to perform statistics, this is going to be more complex. The new hypothesis would then be: given the trials I have recorded from my subjects and given that these trials are a good representation of all the population of trials from the general population of subjects, there is no difference between the ERP/spectrum/ERSP/ITC between the two experimental conditions in the general population of subjects. But the hypothesis is relatively biased because I personally think that all the trials are <b>not</b> a good representation of all the population of trials from the general population of subjects. The trials are a good representation of all the trials from all the subjects being presently recorded but not necessarily of the general subject population. Therefore the real NULL hypothesis would be : given the trials I have recorded from all of my subjects and given that these trials are a good representation of all the population of trials from these subjects, there is no difference between the ERP/spectrum/ERSP/ITC between the two experimental conditions in the recorded subjects. As you see, rejecting the NULL this is relatively limited as we care about the general population of subjects and not the recorded subjects.</div>
<div><br></div><div>If anybody has some better ideas (or Matlab function) of how to handle the subject/trial problem (because it would be nice to include trials in statistical analysis in order to make them more powerful), we will take them.</div>
<div><br></div><div>Best,</div><div><br></div><div>Arno</div><div><br></div><div>ps: we will remove the 'statmode', 'trial' option for now.</div><div>pps: for basic inferential statistics, you may also refer to this book chapter <a href="http://sccn.ucsd.edu/%7Earno/mypapers/statistics.pdf" target="_blank">http://sccn.ucsd.edu/~arno/mypapers/statistics.pdf</a></div>
<div><br></div></div><div><div><div>On Nov 11, 2009, at 12:29 AM, Robert Brown wrote:</div><br><blockquote type="cite">Dear Arno & others,<br><br>this does not seem to be as simple as Arno suggested (but thanks),<br>
<br> 1. I have precomputed the values of these channels (with "savetrials", "on")<br>2. these channels all have data<br> 3. I can plot the data of the same channels when I use "statmode", "subjects"<br>
4. I'm using EEGLAB v7.1.3.13b <br>5. I now tried it with v7.1.7.18b and I still get the log of zero error (you guys might be interested that in addition I now get, in case of permutations and bootstrap, "??? Error using ==> reshape" in statcond>surrogate at 438 and statcond at 301 and with this latest version the reshape error even happens with the "statmode", "subjects")<br>
<br>thus any other suggestions of what could be happening with my single trial analysis in study would be very much appreciated.<br><br>thank you very much and take care,<br>Bob<br> <br><div class="gmail_quote">2009/11/11 Arnaud Delorme <span dir="ltr"><<a href="mailto:arno@ucsd.edu" target="_blank">arno@ucsd.edu</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> Dear Bob,<br> <br> I think this might be because you are trying to plot ERSP of a channel that contains only 0. This error was also arising in old versions of EEGLAB when masking for significance.<br>
<br> Hope this helps,<br> <br> Arno<div><div></div><div><br> <br> On Nov 7, 2009, at 11:38 AM, Robert Brown wrote:<br> <br> </div></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div></div><div> Hi guys,<br> <br> I've been trying to get the study ersp analysis working on single trials but I've not succeeded.<br> <br> in the function "std_readdata" I get the "Warning: Log of zero." error, which is on the line ersp{c,g} = 20*log10(abs(ersp{c,g})); meaning that the absolute value at some point is 0.<br>
(This leads to) further errors:<br> <br> ??? Error using ==> set<br> Bad value for axes property: 'CLim'<br> Values must be increasing and non-NaN.<br> <br> Error in ==> caxis at 80<br> set(ax,'CLim',arg);<br>
<br> Error in ==> tftopo at 714<br> caxis([g.limits(5:6)]);<br> <br> I've tried to fix it but I'm not clever enough. any help would be appreciated.<br> <br> thank you so much,,<br></div></div> Bob <ATT00001.txt><br>
</blockquote> <br> </blockquote></div><br></blockquote></div><br></div></div></blockquote></div><br> </div></div><br>_______________________________________________<br> Eeglablist page: <a href="http://sccn.ucsd.edu/eeglab/eeglabmail.html" target="_blank">http://sccn.ucsd.edu/eeglab/eeglabmail.html</a><br>
To unsubscribe, send an empty email to <a href="mailto:eeglablist-unsubscribe@sccn.ucsd.edu" target="_blank">eeglablist-unsubscribe@sccn.ucsd.edu</a><br> For digest mode, send an email with the subject "set digest mime" to <a href="mailto:eeglablist-request@sccn.ucsd.edu" target="_blank">eeglablist-request@sccn.ucsd.edu</a><br>
</blockquote></div><br><br clear="all"><br>-- <br>Scott Makeig, Research Scientist and Director, Swartz Center for Computational Neuroscience, Institute for Neural Computation, University of California San Diego, La Jolla CA 92093-0961, <a href="http://sccn.ucsd.edu/%7Escott" target="_blank">http://sccn.ucsd.edu/~scott</a><br>
</div> _______________________________________________<br>Eeglablist page: <a href="http://sccn.ucsd.edu/eeglab/eeglabmail.html" target="_blank">http://sccn.ucsd.edu/eeglab/eeglabmail.html</a><br>To unsubscribe, send an empty email to <a href="mailto:eeglablist-unsubscribe@sccn.ucsd.edu" target="_blank">eeglablist-unsubscribe@sccn.ucsd.edu</a><br>
For digest mode, send an email with the subject "set digest mime" to <a href="mailto:eeglablist-request@sccn.ucsd.edu" target="_blank">eeglablist-request@sccn.ucsd.edu</a></blockquote></div><br></div></div><div>
<span style="font-size: 12px;"><div><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><div>
<span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><div style="margin: 0px; min-height: 14px;">
<br><br></div><div style="margin: 0px;">************************************************************************************</div><div style="margin: 0px;"><b style="font-weight: bold;"><span style="font-weight: bold;"><span style="font-weight: bold;"><span style="font-weight: bold;"><span style="font-weight: bold;"><span style="font-weight: bold;"><span style="font-weight: bold;"><span style="font-weight: bold;">Guillaume A. Rousselet, Ph.D.</span></span></span></span></span></span></span></b></div>
<div style="margin: 0px;"><b style="font-weight: bold;"><br></b></div><div style="margin: 0px;"><font face="Arial"><span style="font-family: Helvetica;"><div style="margin: 0px;"><font face="Arial">Lecturer</font></div><div style="margin: 0px;">
<font face="Arial"><br></font></div><div style="margin: 0px;"><font face="Arial">Centre for Cognitive Neuroimaging (CCNi)</font></div><div style="margin: 0px;"><font face="Arial">Department of Psychology</font></div><div style="margin: 0px;">
<font face="Arial"><div>Faculty of Information & Mathematical Sciences (FIMS)</div></font></div><div style="margin: 0px;"><font face="Arial">University of Glasgow</font></div><div style="margin: 0px;"><font face="Arial">58 Hillhead Street</font></div>
<div style="margin: 0px;"><font face="Arial">Glasgow, UK</font></div><div style="margin: 0px;"><font face="Arial">G12 8QB</font></div></span></font></div><div style="margin: 0px;"><font face="Arial"><span style="font-family: Arial;"><br>
</span></font></div><div style="margin: 0px;"><font face="Arial"><div style="margin: 0px;">The University of Glasgow, charity number SC004401</div><div style="margin: 0px;"><br></div></font></div><div style="margin: 0px;">
<span style="font-family: Geneva;"><a href="http://web.me.com/rousseg/GARs_website/" target="_blank">http://web.me.com/rousseg/GARs_website/</a></span></div><div style="margin: 0px;"><font face="Arial"><span style="font-family: Arial;"><br>
</span></font></div><div style="margin: 0px;"><font face="Arial"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;">Email: </span></span></span></span></span></span></span></span></font><a href="mailto:g.rousselet@psy.gla.ac.uk" target="_blank">g.rousselet@psy.gla.ac.uk</a></div>
<div style="margin: 0px;"><font face="Arial"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;">Fax. +44 (0)141 330 4606</span></span></span></span></span></span></span></span></font></div>
<div style="margin: 0px; min-height: 14px;"><font face="Arial"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;">Tel. </span></span></span></span></span></span></span></span></font><font face="Arial"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;">+44 (0)141 330 </span></span></span></span></span><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;">6652</span></span></span></span></span></span></span></span></font></div>
<div style="margin: 0px;"><font face="Arial"><span style="font-family: Arial;"><span style="font-family: Arial;"><span style="font-family: Arial;">Cell +44 (0)</span></span></span></font>791 779 7833</div><div style="margin: 0px;">
<br></div><div style="margin: 0px; min-height: 14px;"><font color="#0000ef"><b style="color: rgb(0, 0, 239); font-weight: bold;"><br></b></font></div><div style="margin: 0px;"><i style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;">"</span></span></span></span></span></span></span></span></span></span></span></span></span></span><span style="font-style: normal;">For reasons I wish I understood, the spectacle of sync strikes a chord in us, somewhere deep in our souls. It's a wonderful and terrifying thing. Unlike many other phenomena, the witnessing of it touches people at a primal level. Maybe we instinctively realize that if we ever find the source of spontaneous order, we will have discovered the secret of the universe.</span></span></i>"</div>
<p style="margin: 0px; min-height: 14px;"><span> </span><br></p><div style="margin: 0px;"><span><span style="white-space: pre-wrap;"><span style="white-space: pre-wrap;"> </span></span>Steven Strogatz -<span> </span><i style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;"><span style="font-style: italic;">Sync</span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></i><span> </span>- 2003</span></div>
<div style="margin: 0px;">************************************************************************************</div><div style="margin: 0px;"><br></div><span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"></span><br>
</span><br></div></span></div></span> </div><br></div></blockquote></div><br>
<br>_______________________________________________<br>
eeglablist mailing list <a href="mailto:eeglablist@sccn.ucsd.edu">eeglablist@sccn.ucsd.edu</a><br>
Eeglablist page: <a href="http://www.sccn.ucsd.edu/eeglab/eeglabmail.html" target="_blank">http://www.sccn.ucsd.edu/eeglab/eeglabmail.html</a><br>
To unsubscribe, send an empty email to <a href="mailto:eeglablist-unsub@sccn.ucsd.edu">eeglablist-unsub@sccn.ucsd.edu</a><br>
To switch to non-digest mode, send an empty email to <a href="mailto:eeglablist-nodigest@sccn.ucsd.edu">eeglablist-nodigest@sccn.ucsd.edu</a><br></blockquote></div><br>