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mixOmicsTeam / mixOmics

Development repository for the Bioconductor package 'mixOmics '
http://mixomics.org/
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tranform before PCA? #312

Closed marwa38 closed 1 month ago

marwa38 commented 2 months ago

Hi team Do you recommend to run log tranform the data before visualising using PCA? or even PLSDA? knowing that the data is normalised. Especially when the data is not meeting the parametric assumptions that PCA requires.

I ran permanova on the results and I got no significant difference between male and female groups although PLSDA showed seperation? image

Please let me know Marwa

evaham1 commented 1 month ago

Hi @marwa38 please use our mixOmics discussion forum for any questions about analysis (we only use Github issues for bug reports), you might find other people have posted a similar question to yours on there - https://mixomics-users.discourse.group/