[Eeglablist] Codes for cluster correction are needed

[Olivia Yang]

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
>>>>> _______________________________________________
>>>>> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
>>>>> To unsubscribe, send an empty email to
>>>>> eeglablist-unsubscribe at sccn.ucsd.edu
>>>>> For digest mode, send an email with the subject "set digest mime" to
>>>>> eeglablist-request at sccn.ucsd.edu
>>>>
>>>> --
>>>> 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
>>
>> https://urldefense.com/v3/https://cpernet.github.io/;!!Mih3wA!BrNn2j4iKMeFLS6PS8IC6f7nRqK9ye2CG39s_8-u6R209tyg6NpxXExCVvR9z9g0EU9_RjUBrWmEr2UdSb0_VA$
>>
>> https://urldefense.com/v3/https://orcid.org/0000-0003-4010-4632;!!Mih3wA!BrNn2j4iKMeFLS6PS8IC6f7nRqK9ye2CG39s_8-u6R209tyg6NpxXExCVvR9z9g0EU9_RjUBrWmEr2Vu9feMUA$
>>
>> --
>> 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
>>
>> https://urldefense.com/v3/https://cpernet.github.io/;!!Mih3wA!BrNn2j4iKMeFLS6PS8IC6f7nRqK9ye2CG39s_8-u6R209tyg6NpxXExCVvR9z9g0EU9_RjUBrWmEr2UdSb0_VA$
>>
>> https://urldefense.com/v3/https://orcid.org/0000-0003-4010-4632;!!Mih3wA!BrNn2j4iKMeFLS6PS8IC6f7nRqK9ye2CG39s_8-u6R209tyg6NpxXExCVvR9z9g0EU9_RjUBrWmEr2Vu9feMUA$
>>
>> _______________________________________________
>> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
>> To unsubscribe, send an empty email to
>> eeglablist-unsubscribe at sccn.ucsd.edu
>> For digest mode, send an email with the subject "set digest mime" to
>> eeglablist-request at sccn.ucsd.edu
>
> _______________________________________________
> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
> To unsubscribe, send an empty email to eeglablist-unsubscribe at sccn.ucsd.edu
> For digest mode, send an email with the subject "set digest mime" to eeglablist-request at sccn.ucsd.edu