neurorestore/Libra

NA values when using mixedmodel for deg identificaiton.

HelloWorldLTY opened this issue · 0 comments

Hi, I try to use mixed model for deg analysis, but all the statistics I have here are NA.
image

My codes are:

library(Seurat)
library(fgsea)
source('sex_specificity_helper.R')
library(stats)
library(Libra)

data = readRDS("data.rds")

data$replicate = data$sample
data$cell_type = data$gender
data$label = data$condition

DE = run_de(data, de_family = 'mixedmodel', de_method = "negbinom", n_threads = 12)

head(DE)

saveRDS(DE, "mixedmodelall.rds")

I am also confused abou the de_family name, why it is pseudobulk not mixed model? Thanks a lot.