CLR assay missing in scADT-All-Hematopoiesis-MPAL-191120.rds

[rargelaguet]

scADT-All-Hematopoiesis-MPAL-191120.rds contains the rawCounts but not the CLR normalised assay.
I tried applying compositions::clr as well as the CLR transformation implemented in Seurat :

clr_function <- function(x) { 
 return(log1p(x = x / (exp(x = sum(log1p(x = x[x > 0]), na.rm = TRUE) / length(x = x)))))
}

but I cannot reproduce the normalisde values in the CLR assay from scADT-Healthy-Hematopoiesis-191120.rds. Could you add the code that you used for the CLR normalisation?

Thank you,
Ricard.

[jgranja24]

i used Seurat's default CLR normalization

https://satijalab.org/seurat/v3.0/multimodal_vignette.html

let me know if that helps