[Eeglablist] Codes for cluster correction are needed

Thu Jul 28 00:57:49 PDT 2022

I don't see how that code would work ?? Olivia's data are 
Subjects*Conditions*Channels for peak values

just switch dim to please the code Channels * Subjects say cond1 vs 
cond2, the difference cannnot create good clster over space because 
channel is vectorized and thus can be organized in any way possible

sorry Olivia - I'm pretty sure it won't work ...
cyril

On 27/07/2022 16.16, Olivia Yang via eeglablist wrote:
> Hi Makoto,
>
> Thank you very much!
>
> Sorry to bother you, but I have the following questions:
>
> 1. Are there demo codes for this solution to do two-factor repeated ANOAV?
>
> If not, am I correct with my try:
>
>> %%%%%%%
>>
>> %%%%%%%
>>
>> %%%%%%%
>>
>> %%%%%%%
>>
>> for c=1:4
>>
>> input{i}=squeeze(PeakValue(c,:,:)); % PeakValue is a three dimensional matrix (Experimental conditions × Channels × Subjects) of peak values picked out from N170；
>>
>> % Four experimental conditions belong to two factors：
>>
>> %input{1} is the date for level 1 of factor A and level 1 of factor B
>>
>> %input{2}, level 2 of factor A and level 1 of factor B
>>
>> %input{3}, level 1 of factor A and level 1 of factor B
>>
>> %input{4}, level 2 of factor A and level 2 of factor B
>>
>> end
>>
>> repeatedMeasuresFlag= 3; % random-effect test
>>
>> pValForPreselection=0.05; % Is the p-value before or after cluster correction needed here? Is there a recommended setting for this parameter?
>>
>> numIterations=10000;
>>
>> [mask, tScore, pValue] = clusterLevelPermutationTest2x2(input{1}, input{2), input{3}, input{4}, repeatedMeasuresFlag, pValForPreselection, numIterations);
>>
>> %%%%%%%
>>
>> %%%
>>
>> %%%%%%%
>>
>> %%%%%%%
>>
>> %%%%%%
> 2. About the outputs of this funtion, I don’t know which parts indicate the cluster correction results of the interaction effect or the main effects of ANOAV analysis.
>
> 3. Are not channel locations needed as inputs? That makes me wonder how this function conducts multiple comparison corrections across space without channel location information.
>
> Best regards,
>
> Olivia
>
> ------- Original Message -------
> Makoto Miyakoshi via eeglablist eeglablist at sccn.ucsd.edu wrote:
>
>> Dear Olivia,
>>
>> In case you be interested in my solution, see the following code for your
>> info.
>> https://urldefense.com/v3/https://github.com/sccn/groupSIFT/blob/master/clusterLevelPermutationTest.m;!!Mih3wA!FcwOZGypevvYbX4NXfyvIOJRXVzzgjj1amwOZGA8N4-LyVn9QVPYjt9Qj-zN-qeE36ZGpxTN1zdSmayiorkXQOSfAbQ$
>>
>> Makoto
>>
>> On Thu, Jul 21, 2022 at 11:35 AM Dr Cyril, Pernet via eeglablist <
>> eeglablist at sccn.ucsd.edu> wrote:
>>
>>> Hi Olivia,
>>>
>>> You can in principle do clustering under 1 dimension only using
>>>
>>> https://urldefense.com/v3/https://github.com/LIMO-EEG-Toolbox/limo_tools/blob/master/limo_clustering.m;!!Mih3wA!BrNn2j4iKMeFLS6PS8IC6f7nRqK9ye2CG39s_8-u6R209tyg6NpxXExCVvR9z9g0EU9_RjUBrWmEr2UUzu6Ayw$
>>>
>>> - but you will have to generate the bootstrap or permutation data under
>>> the null. I am really not sure that this would be less conservative than
>>> FDR in such a case though.
>>>
>>> Cyril
>>>
>>>> Hi Cyril，
>>>>
>>>> Thank you very much for your kind reply with detailed explanations!
>>>>
>>>> However, FDR correction is too conservative in my case. So, I’d like to
>>>> use alternative correction methods that can take space information into
>>>> consideration.
>>>>
>>>> I thought it would be easy to finish cluster corrections for peak
>>>> amplitude statistics in EEGLAB. But it looks like not.
>>>>
>>>> Best wishes,
>>>> Olivia
>>>>
>>>> ------- Original Message -------
>>>> On Wednesday, July 20th, 2022 at PM 3:18, Dr Cyril, Pernet <
>>>> wamcyril at gmail.com> wrote:
>>>>
>>>>> Hi Olivia
>>>>>
>>>>> clustering requires some continuity over space and/or time - here you
>>>>> have a 30 (Subjects) × 4 (Conditions in my experiment) × 66 (Channels)
>>>>> matrix of peak values so could cluster over space but I would really not
>>>>> recommend doing that as these a 'peaks' so really different measurements
>>>>> at each channels - in your case I'd test whatever differences you are
>>>>> interested in and apply an FDR correction.
>>>>>
>>>>> more info from a good old EEGLAB lecture
>>> https://urldefense.com/v3/https://figshare.com/articles/presentation/Statistical_analysis_of_EEG_data_Hierarchical_modelling_and_multiple_comparisons_correction/4233977;!!Mih3wA!BrNn2j4iKMeFLS6PS8IC6f7nRqK9ye2CG39s_8-u6R209tyg6NpxXExCVvR9z9g0EU9_RjUBrWmEr2Wvu8_cjQ$
>>>
>>>>> slides 2 and 3 gives you an idea why I'd not recommend your approach
>>>>> above and slides 24+ explains multiple comparison corrections and among
>>>>> those procedure, clustering.
>>>>>
>>>>> reference article
>>> https://urldefense.com/v3/https://www.sciencedirect.com/science/article/pii/S0165027014002878;!!Mih3wA!BrNn2j4iKMeFLS6PS8IC6f7nRqK9ye2CG39s_8-u6R209tyg6NpxXExCVvR9z9g0EU9_RjUBrWmEr2WxKJjPFg$
>>>
>>>>> cyril
>>>>>
>>>>>> Dear EEGLAB geniuses,
>>>>>>
>>>>>> Do you know whether there are codes for performing cluster corrections?
>>>>>>
>>>>>> After I finished the preprocessing analysis in EEGLAB, I picked out
>>>>>> peak values of N170 from average waveforms through custom Matlab codes. And
>>>>>> a 30 (Subjects) × 4 (Conditions in my experiment) × 66 (Channels) matrix of
>>>>>> peak values was generated. Afterwards, I conducted repeated measure ANOVA
>>>>>> and got statistical values of each channel.
>>>>>>
>>>>>> Now I need to perform multiple comparison corrections (cluster
>>>>>> correction) for the comparison of peak value difference among the four
>>>>>> conditions. Are there codes or more effortless ways that can help me?
>>>>>>
>>>>>> Looking forward to your reply!
>>>>>>
>>>>>> Cheers!
>>>>>>
>>>>>> Best regards,
>>>>>>
>>>>>> Olivia
>>>>>> _______________________________________________
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>>>>> --
>>>>> Dr Cyril Pernet, PhD, OHBM fellow, SSI fellow
>>>>> Neurobiology Research Unit,
>>>>> Building 8057, Blegdamsvej 9
>>>>> Copenhagen University Hospital, Rigshospitalet
>>>>> DK-2100 Copenhagen, Denmark
>>>>>
>>>>> wamcyril at gmail.com
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>>>
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>>>
>>> --
>>> Dr Cyril Pernet, PhD, OHBM fellow, SSI fellow
>>> Neurobiology Research Unit,
>>> Building 8057, Blegdamsvej 9
>>> Copenhagen University Hospital, Rigshospitalet
>>> DK-2100 Copenhagen, Denmark
>>>
>>> wamcyril at gmail.com
>>>
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>>>
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>>>
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-- 
Dr Cyril Pernet, PhD, OHBM fellow, SSI fellow
Neurobiology Research Unit,
Building 8057, Blegdamsvej 9
Copenhagen University Hospital, Rigshospitalet
DK-2100 Copenhagen, Denmark

wamcyril at gmail.com
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