Hello, I am new to the mixOmics and this is my first time posting my question in the forum.

I am working on a swine project and plan to use multi-omics to predict the phenotype of pigs.

For the data I have: 836 samples with phenotype, transcriptome (~15000), proteome(~400), and metabolome(~50). First I plan to use the single omics data to predict the phenotype. I found PLS-DA can do this job and tried what the tutorial suggests. I tried “perf” function to estimate how many components I should use for this study and the results for transcriptome was shown below:

single transcriptome:

Based on these results, I have no idea how many components I should use in my study. Can you give me some ideas about the results?

Another question, can we fit more factors in the model when we use the function plsda? For example, I know the batch is another factor affecting the phenotype, how to fit these kind of factors in the model when we use plsda.

Looking forward to your reply!

Best regards,

Yulu