How to identify down-regulated genes in monocle

Question

[tujuchuanli]

Hi, all

Here I used “differentialGeneTest” in monocle to identify differentially expressed genes (DEGs) when analyzing scRNA-seq data.

My question is how to mark up/down-regulated genes or there are only up-regulated genes to be identified when using “differentialGeneTest” in monocle? If so how do I identify down-regulated genes?

Below is some codes in my analysis:

group[which(group == "treated")] = 1
group[which(group == "control")] = 2
HSMM_for_DE$group = group
HSMM_for_DE$group = as.numeric(HSMM_for_DE$group)
HSMM_for_DE = estimateSizeFactors(HSMM_for_DE)
HSMM_for_DE = estimateDispersions(HSMM_for_DE)
diff_test_res = differentialGeneTest(HSMM_for_DE, fullModelFormulaStr = "~group", cores = 10, verbose = F)

Here I tried to switch label for treated and control (from “1 for treated and 2 for control” to “2 for treated and 1 for control”). However the output is the same as the one before switching

Answer 1

[tujuchuanli]

Does anyone know how to identify down-regulated genes by monocle?