[Eeglablist] Codes for cluster correction are needed

[Makoto Miyakoshi]

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
> >>
> 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$
>
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