help with alra

[mocherry]

Dear all,

I am kind of lost how to deal with the results of ALRA.
When I process a Seurat object with ALRA I get a new assay. How do I then use the ALRA computed data to do a UMAP or TSNE reduction based on these data? Seems that whatever I do the result of both looks the same as the one produced by the standard pipeline after SCTransform.

I would greatly appreciate a jump start in this matter.

Thanks and best,
Matthias

[ggruenhagen3]

If you did what I did and added the imputed data matrix into the data slot of the SCT assay then performed RunPCA and downstream analysis and then were confused about why nothing changed - I can explain. The PCA is dependent of the scaled data and if you did what I did, then the scaled data was not modified at all and thus the PCA and downstream analysis wasn't affected. I can't think of a way to use ALRA and to use SCTransform together (at least correctly for the latter).

The code below is not a solution. This is what I did, which leads to no change due to the reasons I outlined above. This code is meant for reproducibility and clarity.

# NOT A SOLUTION
alra_res = ALRA::alra(data_mat)
data_mat_imp = alra_res[[3]]
data_mat_imp = t(data_mat_imp)
colnames(data_mat_imp) = colnames(big_obj)
big_obj[["SCT"]]$data = as(data_mat_imp, "dgCMatrix")
big_obj = RunPCA(big_obj, assay = "SCT")
...