How to design rows in the input of single-cell multi-omics data

Analysis
2

Hi @QuietgraceH,

Thanks for using mixOmics!

  1. Yes, if you want to integrate your modalities and identify features that distinguish your states (normal vs disease) you can use DIABLO. If you want to integrate your datasets only within samples collected from normal or disease group you can use multiblock (s)PLS.
  2. Sparsity is a common issue with single cell data, and whilst the mixOmics realm doesn’t extend to dealing with sparsity, there are lots of other tools out there that you can use to address this. One example would be grouping cells into metacells, a recent user on the forum asked a similar question - have a look at the suggestions there.
  3. The number of folds to choose depends on your number of samples, which will depend on point 2. In general we recommend choosing folds that include at least 5-6 samples, see more details here.

Hope that helps!
Eva