I want to perform O2PLS-DA analysis of multiomics data (from different metabolomics lipidomics and proteomics experiments) by using SIMCA 130.2? I have data in matrix format (samples in row with labels and variables in column). I can perform upto PCA, PLS-DA and OPLS-DA, but the O2PLS-DA tab is not active. I think I do have a problem with data arrangement. However, not sure if its the only problem. Any help will be highly appreciated!
Unlike all methods you listed there, O2PLS-DA requires two datasets. If you have three, you need to specify which pairs you want to use!
Thank you Francisco! I have 6 independent dataset actually. I was combining them in a single datashet, initially. Will it be feasible?
If you want to integrate the six of them in one go I would rather use multiple co-inertia analysis, regularized generalized CCA or STATIS. Refer to Meng et al. 2016:
https://academic.oup.com/bib/article/17/4/628/2240645
I personally dislike SIMCA, it is highly limited. In any case I presume you have to provide two separate matrices at a time for O2PLS-DA. As for the other methods, you can run PCA, PLS-DA, etc. on the entire thing - however note that you run the risk of contaminating results with the technical noise specific to each separate omics readout. Hope this is clear? Cheers
- Badges
- Science topic
- Similar topics
- Chemistry
- General Biochemistry
- Proteomics