<p>I have a binary matrix with individuals as row names, and gene name as column name.
So, if the gene is present in an individual, we have 1, otherwise 0.</p>
<p>I would like to cluster individuals based on the gene presence/absence pattern.</p>
<p>Is it right to perform an MCA? Or a logistic PCA is needed?</p>
<p>Thanks,
Marco</p>

CC BY-SA 4.0
2022-10-14T14:41:42.877Z
Would you consider hierarchical clustering, i.e. making a tree? However you need to present a test data set and I could give you the tree with an explanation. PCA is okay, but trees have advantages, for reasons I could explain.
M__
CC BY-SA 4.0
2022-10-22T11:26:11.843Z
I believe the answers to your question are here:
https://help.ezbiocloud.net/gene-presenceabsence-analysis/
https://www.biostars.org/p/66355/
Avamys
<r><clustering><pca>
Clustering individuals by gene presence/absence
# Clustering individuals by gene presence/absence

(Asked by: username_0 on 2022-10-14)

I have a binary matrix with individuals as row names, and gene name as column name.
So, if the gene is present in an individual, we have 1, otherwise 0.

I would like to cluster individuals based on the gene presence/absence pattern.

Is it right to perform an MCA? Or a logistic PCA is needed?

Thanks,
Marco

**Tags:** r, clustering, pca
> **Comments:**
> **username_1**: Would you consider hierarchical clustering, i.e. making a tree? However you need to present a test data set and I could give you the tree with an explanation. PCA is okay, but trees have advantages, for reasons I could explain.  
> **username_2**: I believe the answers to your question are here: https://help.ezbiocloud.net/gene-presenceabsence-analysis/ https://www.biostars.org/p/66355/  

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