Hii,
I am a student and just started using the mixomics package for carrying out the integration of my proteomics and metabolomics datasets. So, i have 6 samples, 3 of control and 3 of coculture at 2 timepoints. Same for both the omics data set having the area intensities values in my matrix. So how should i design my rCCA analysis for small sample size.
Hi @Anushka,
I am not sure if I’ve completely understood your experimental design, but assuming you have 6 samples: 3 control and 3 coculture, and you want to identify which features in your proteomics and metabolomics data which distinguish control versus coculture, I would suggest using DIABLO. You can read more about DIABLO here and have a look at a case study using DIABLO here. rCCA is an unsupervised approach, so it would allow you to integrate your proteomics and metabolomics data but it won’t tell you about the differences between your control and coculture groups.
Hope that helps!
Eva