If I have two groups of small molecules with different properties, e.g. one can penetrate membranes and the other cannot, and I have an m × n matrix of m small molecules and n descriptors (e.g. polar surface area, molecular weight), can I use, say, limma to identify descriptors that differ between these two groups? So basically, I would just be using limma on molecular descriptors instead of gene expression data. If it makes any difference, some of these descriptors are discrete (e.g. number of rotatable bonds) and some are continuous (e.g. weight.)
If so, would I have to prepare the data in any special way? If not, what algorithms would be best for this sort of task?