Elham

Just a quick update to add: I can run `FindTransferAnchors(...)` when I use default values for parameter weight.reduction. But when I use `FindTransferAnchors(weight.reduction = "cca", ...)` for integration, I get...

Thanks for getting back to me! Sure, I have my Rscript in the following using Ref: https://satijalab.org/seurat/articles/pbmc3k_tutorial.html#####setup-the-seurat-object-1 >library(dplyr) library(Seurat) library(patchwork) library(Signac) library(EnsDb.Hsapiens.v86) #####setwd("~/Downloads/alignment/Seurat/") ##### Load the RNA dataset >rna.dir

Hi @cgao90 Thank you very much for getting back to me. Yes, I checked on that and my RNA and ATAC are both genes by cells matrices. Do you possibly...

Follow-up: I have tried the following code to generate them, would you mind checking if this is the desired approach to get the files? Thank you in advance! ``` if...

Just a follow-up on this: LIGER performs fine on this dataset and generates reasonable latent space for RNA and ATAc, but using iNMF, I get trivial zero latent values in...

Hi @jw156605 thank you for your response. Yes, that is correct.

Hello @joschif Thank you for the detailed tutorials! I have a similar issue to the one reported above. I followed the tutorials and at this part of the code, I...

Hello @joschif I am updating this issue. I tried keeping common cells within both assays so now both my RNA and ATAC data have 557 cells. The error I get...

Thanks @joschif! Yes, this is correct that `Matrix` package was problematic. Following [this solution](https://github.com/satijalab/seurat/issues/8202) and [this one](https://github.com/quadbio/Pando/issues/53#issuecomment-1901660078) worked for me if anyone faced this issue in the future. Also, I...