I have a dataset with two modalities (RNA, protein) which I want to analyze using TOTALIV. I am more familiar with R so ideally I would like to run the model in Python and then transfer the latent repsresentations and denoised counts to continue my analysis there. I went through the user guide and I have a couple of questions that I needed some clarifications. I attach them below for anyone who may be able to assist:
- how can one store the protein raw counts in the adata file? It is obvious for the RNA counts
adata.layers[“counts”] = adata.X.copy()
but not for the protein ones.
Is it possible to extract the denoised counts for RNA, proteins to add in a Seurat object?
Is it possible to calculate DE genes/proteins for each of the clusters AND one additional condition? For example, cluster 1 stim vs ctrl? I can see that this information can be filled in the
argument, but I understand this can only apply for a one vs all comparison.
Thanks very much in advance,