Hello! First attempt at mixomics and I was wondering if anyone can help with the right model to use. I have paired samples (neutrophils from 5 separate individuals, each individual split into two treatments - control and infected), and I have RNA-Seq, miRNA microarray data and methylation data (RRBS-Seq). Our main interest is seeing the effect of infection in an integrated manner. My understanding is that I could use DIABLO, but if this is correct, how do I make sure that samples are paired (control and infected cells from each individual). Thanks in advance 
Hi @fllopes,
For paired samples you may want to have a look at a multilevel decomposition per dataset, as shown here: Multilevel – mixOmics
If you think multilevel is the way to go, then apply this decomposition (it is akin to a processing step) for each data set, then input into DIABLO. We recommend you first explore each data set individually (with PCA, PLS-DA and multilevel) first before you move to integration.
Kim-Anh