> I work on a similarity matrix, representing interaction frequencies between
> regions of DNA. I have two types of missing data. The first one is that we do
> not have enough cells to have a measure. It means that the two regions are far
> away from each other. The second one is due to repetitions in the DNA sequence.
> In both case, I can infer the missing data, but the inference is very
> different.

It sounds to me like you need to imputations, not a different fit and
transform. Am I wrong?

G