differentially expressed genes

[feanaros]

Hi developers! Thank you for this wonderful package! a very basic question I have. Is it possible to find differentially expressed genes using getmarkerfeatures?

markersGS <- getMarkerFeatures(ArchRProj = archrproject,
useMatrix = "GeneIntegrationMatrix",
groupBy = "Clusters",
usegroups= "Red_KO",
bdgGroups= "Red_WT"
bias= c("TSSEnrichment", "log10(nFrags)"),
testMethod = "wilcoxon",
binarize = F,
maxCells = 1000)

markerList_genes <- getMarkers(markersGS, cutOff = "FDR <= 0.05 & Log2FC >= 0.5")
The markerlist genes resulting contains empty rows and 9 column. Where I'm wrong? Thanks!!!!!
F

[rcorces]

Please note that this is not an Issue, but a Discussion and should have been posted there.
Presumably, the filters you have set via cutOff result in zero pass-filter features.

[feanaros]

Ok, with a less stringent cutoff, I found 0 features. I saw that FDR are higher than 0.5, so presumably the genes are not statistically significatives. However, with Seurat I found at least 20 DE genes setting the cutoff very stringent, so I cannot explain that. The integrationMatrix comes from the same scRNAseq that I used for Seurat.