Pierre-Luc

Hi @lshep , I'm just curious about your comment that "Bioconductor would like a clean repository on our system." Does that mean you want it clean _only_ for the submission?...

Dear @lshep , We discussed together regarding this point: > Your functions should work directly with SpatialExperiment Objects rather than extracting data frames. You should be able to store results...

Hi, No renaming the column won't help, right now it's not possible to specify 2 random effect variables. How are the individuals spread across the batches? If you have large...

Hi, of course you can do that, but you lose the uncertainty related to the effect of the covariates you correct for, which is dangerous. This is getting into an...

Hi, BPPARAM is not used when there's a single sample, hence the analyses are all working with different seeds.

Hi, I'm afraid I don't have a great answer beyond educated guess. The aim of FDR correction is to control for FDR (disregarding type II errors), but with doublet identification...

This isn't unreasonable, if quite strict. With multimodal data, I think there's a value in combining scores from the two modalities before calling doublets, but how exactly to best do...

Hi, I agree. The main drawback of using amulet on its own is that it doesn't work well with cells that have a low library size, so that's why we...

Hi, 1. Please clarify what you mean by "delete the cells that are both double cells twice." 2. It's common (especially if the artificial doublets are random) for some singlet...

1. Sounds good. So indeed the UMAP was misleading, and your doublet scores are very bimodal, as they should be.