I want to integrate RNA with protein abundance, and I have multiple REAP-seq samples. My approach was to
fastMNN the RNA data, and get clusters with the corrected values. Then I thought I could also MNN correct the ADT data, and then match both clusterings. Or maybe do "subclustering" as described in the OSCA book.
My question is if I can actually integrate the ADT samples with
fastMNN, what I tried so far is:
#d is a sce with normalized ADT in the altExp() altExp(d) <- multiBatchNorm(altExp(d), batch = batch) mnnadt.out <- fastMNN(altExp(d), batch = batch, d = 37, cos.norm = FALSE, BSPARAM=BiocSingular::RandomParam(deferred=TRUE), BPPARAM=MulticoreParam(3))
but this does PCA under the hood right? but since I only have 37 markers, I don't need to reduce dimensionality. While I'm writing this I realize I could put
d=NULL as in
Thank you, Stephany