[FieldTrip] ft_freqstatistics and FDR-correction
Patricia Wollstadt
Patricia.Wollstadt at gmx.de
Tue Feb 1 16:34:04 CET 2011
Hi Michael, Hi Jan-Mathijs,
thank you very much for the advice/clarification. Everything seems to run fine now (with the corrected design).
Thank you very much,
Best
Patricia
-------- Original-Nachricht --------
> Datum: Wed, 26 Jan 2011 10:08:51 +0100 (CET)
> Von: "Michael Wibral" <michael.wibral at web.de>
> An: "Email discussion list for the FieldTrip project" <fieldtrip at donders.ru.nl>
> Betreff: Re: [FieldTrip] ft_freqstatistics and FDR-correction
> Hi Patricia,
>
> I also would have thought your design to be correct. Maybe the
> unneccessary specification of the uvar screws thinsg up??
>
> However, you really do not have any repeated measures in your design -
> here the output of FT is correct. I interpret it in the following way: You
> specified cfg.uvar - indicating to FT the possibility that this might be a
> repeated measures design. FT identified the units of observation as being 80
> (correct), and then checked how many repeated measures you ran in each UO
> and found just 1 - which is also correct. I agree that naming the units of
> observation (UO) as 'levels' of the UO variable is a bit odd, should rather
> be 'units of observation'.
>
> The concept of repeated measures is also very often misunderstood: in
> repated measures you do not actually repeat anything, rather you perform
> different measurements (treatments) WITHIN a unit of observation - so a repated
> measures design is a within UO design. Your subjects just have one age, so
> there are no different treatments (levels of the indep variable) per
> subjects and, hence, no 'repeated measures'.
>
> Hope this clarifies terminology for further discussion.
>
> Michael
>
>
> -----Ursprüngliche Nachricht-----
> Von: "jan-mathijs schoffelen" <jan.schoffelen at donders.ru.nl>
> Gesendet: Jan 25, 2011 8:57:03 PM
> An: "Email discussion list for the FieldTrip project"
> <fieldtrip at donders.ru.nl>
> Betreff: Re: [FieldTrip] ft_freqstatistics and FDR-correction
>
> >Hi Patricia,
> >
> >I don't really understand what is going on, but could you try to
> >specify your design only in a single row (design = design(2,:) in your
> >case), specify cfg.ivar = 1; and cfg=rmfield(cfg,'uvar'), and see how
> >it runs? As such the uvar row is not relevant in an independent
> >samples design.
> >
> >Best,
> >
> >Jan-Mathijs
> >
> >
> >
> >On Jan 25, 2011, at 6:08 PM, Patricia Wollstadt wrote:
> >
> >> Dear all,
> >>
> >> I'm still trying to identify the underlying reason for the issue
> >> described below. I ran the analysis in debug mode (I'm using
> >> Matlab2008b and the Fieldtrip-release from the 16th of January 2011)
> >> and found that the matrix 'resample', that is generated in
> >> 'statistics_montecarlo', line 187:
> >>
> >> resample = resampledesign(cfg, design);
> >>
> >> doesn't contain actual permutations of my initial design, but rather
> >> sorted rowvectors from 1 to 80 (no of subjects). So (since there is
> >> no permutation of the units of observation) the 'randstat' that is
> >> subsequently calculated for each row of the resample-matrix is
> >> always the same.
> >> Is this maybe due to my design and my units of observations
> >> respectively? I am looking at age-dependent variations in resting-
> >> state data, so my UO are 80 subjects, divided into four age groups.
> >> The commandline-output of the 'resampledesign'-function is as follows:
> >>
> >> total number of measurements = 80
> >> total number of variables = 2
> >> number of independent variables = 1
> >> number of unit variables = 1
> >> number of within-cell variables = 0
> >> number of control variables = 0
> >> using a permutation resampling approach
> >> repeated measurement in variable 1 over 80 levels
> >> number of repeated measurements in each level is 1 1 1 1 1 1 1 1 1 1
> >> 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
> >> 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
> >> 1 1
> >>
> >>
> >> Is this correct? Shouldn't this read 'repeated measurement in
> >> variable 2 over 4 levels' with the number of subjects per group as
> >> repeated measurements within a condition? Still I am pretty sure
> >> about my design matrix, which contains the indices 1 to 80 (for all
> >> subjects) in the first row (this is my cfg.uvar) with the
> >> corresponding age groups (1 to 4) in the second row (cfg.ivar, see
> >> my previous email below). I use an 'indepsamplesF'-statistic, since
> >> I am comparing between four groups of different subjects (averaged
> >> over trials).
> >>
> >> I hope, I got the settings and my design right. Any suggestions,
> >> whether this is a problem due to wrong configurations in my script
> >> are very welcome.
> >>
> >> Right now I work around this issue by replacing line 279 in
> >> 'statistics_montecarlo':
> >>
> >> tmpdesign = design(:,resample(i,:));
> >>
> >> with:
> >>
> >> tmpdesign = design(:,randperm(size(design,2)));
> >>
> >> creating permutations of my design 'by hand'. Is this acceptable or
> >> is there anything I'm maybe missing.
> >>
> >> Thank you very much, kind regards,
> >>
> >> Patricia
> >>
> >>
> >>
> >>
> >> -------- Original-Nachricht --------
> >>> Datum: Mon, 24 Jan 2011 17:47:26 +0100
> >>> Von: "Patricia Wollstadt"
> >>> An: fieldtrip at donders.ru.nl
> >>> Betreff: [FieldTrip] ft_freqstatistics and FDR-correction
> >>
> >>> Dear Fieldtrip-users,
> >>>
> >>> I'm currently trying to calculate freqstatistics for four
> >>> experimental
> >>> groups, using the following options:
> >>>
> >>> groupSize=[length(subjects{1}) length(subjects{2})
> >>> length(subjects{3})
> >>> length(subjects{4})];
> >>>
> >>> design = [1:groupSize(1)+groupSize(2)+groupSize(3)+groupSize(4)];
> >>> % 1 to N subjects
> >>> design(2,:) = [ones(1,groupSize(1)) 2*ones(1,groupSize(2))
> >>> 3*ones(1,groupSize(3)) 4*ones(1,groupSize(4))]; % indep var ->
> >>> group membership
> >>>
> >>>
> >>> cfg=[];
> >>> cfg.design=design;
> >>> cfg.uvar = 1;
> >>> cfg.ivar = 2;
> >>> cfg.method = 'montecarlo';
> >>> cfg.statistic = 'indepsamplesF';
> >>> cfg.correctm = 'fdr';
> >>> cfg.numrandomization = 180000;
> >>> cfg.alpha = 0.01/7;
> >>> cfg.tail = 1;
> >>> cfg.design = design;
> >>> cfg.channels = myChannels;
> >>> cfg.avgovertime = 'yes';
> >>> cfg.avgoverfreq = 'yes';
> >>> cfg.frequency = [1 3];
> >>>
> >>> stat = ft_freqstatistics(cfg, group1avg, group2avg, group3avg,
> >>> group4avg);
> >>>
> >>> With these settings, the coputation itself runs fine, but the
> >>> resulting
> >>> 'prob'-matrix contains only zeros (accordingly the 'mask'-matrix
> >>> consists of
> >>> only ones). This would mean, that I found significant effects for all
> >>> channels. Is this possible or rather due to an error somewhere in
> >>> my script? Is
> >>> it likely, that these are 'real' zeroes or rather very small
> >>> values, close
> >>> to zero?
> >>> Any hints and suggestions are very welcome, thank you in advance,
> >>>
> >>> Kind regards
> >>>
> >>> Patricia Wollstadt
> >>>
> >>>
> >>> --
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> >>
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> >> _______________________________________________
> >> fieldtrip mailing list
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> >
> >Dr. J.M. (Jan-Mathijs) Schoffelen
> >Donders Institute for Brain, Cognition and Behaviour,
> >Centre for Cognitive Neuroimaging,
> >Radboud University Nijmegen, The Netherlands
> >J.Schoffelen at donders.ru.nl
> >Telephone: 0031-24-3614793
> >
> >_______________________________________________
> >fieldtrip mailing list
> >fieldtrip at donders.ru.nl
> >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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