Using Seurat function `FindMarkers` to find differentially expressed genes between normal group and treatment group within one specific cell type cluster, but the avg_log2FC results looks weird?


I have two groups scRNAseq data, and I have finished cell type annotation. Now I would like to find the differentially expressed genes between two condition groups(normal vs treatment) within one cell type cluster, and I used Seurat function FindMarkers as follows hoping to find the DEGs across different conditions (Normal vs Treatment)

Alveolar.macrophages.response <- FindMarkers(normal.vs.Veh, ident.1 = "Alveolar macrophages_Normal", ident.2 = "Alveolar macrophages_Veh", verbose = FALSE)

However, I have some concerns about the returned results from FindMarkers, I used head(Alveolar.macrophages.response[with(Alveolar.macrophages.response, order(avg_log2FC, decreasing = T)), ], 5) to display the results with respect to the decreasing order of avg_log2FC. The avg_log2FC are in general very small, even the largest value of avg_log2FC only up to 0.9793757 which looks very weird to me comparing to what I saw on many other tutorials. I wonder whether this result is reasonable?

                       p_val avg_log2FC pct.1 pct.2     p_val_adj
Tm4sf19        3.630080e-153  0.9793757 0.203 0.079 7.161784e-149
Slfn4           8.873470e-65  0.6886944 0.398 0.290  1.750647e-60
LOC100360087   9.405795e-295  0.6689990 0.935 0.839 1.855669e-290
Fth1           4.259850e-230  0.5818955 0.963 0.896 8.404258e-226
Fkbp5          7.286612e-134  0.5672482 0.406 0.249 1.437576e-129
Hmox1           1.944299e-91  0.5299588 0.291 0.174  3.835907e-87
Zdhhc14         9.329413e-77  0.5016266 0.567 0.455  1.840600e-72





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