Barplot of genes deferentially expressed in a few clusters

Question

[mvis1231]

Hi I have two samples (control and knockout) of scRNA-seq data and I followed Seurat vignette to do the integrative analysis (https://satijalab.org/seurat/v3.2/immune_alignment.html).

I tried to find some genes with increased/decreased expression in clusters by comparing their "Avg_logFC" values for KO and control, but all I can see is the "Avg_logFC" values between the two samples are symmetric, and I cannot see the increase/decrease in expression of gene between the samples per cluster.

The code that I tried to pull up the "Avg_logFC" values was:

c3.KO_markers <- FindMarkers(integrated, ident.1 = "Knockout", group.by = 'sample', subset.ident = "3")  
c3.Ctn_markers <- FindMarkers(integrated, ident.1 = "Control", group.by = 'sample', subset.ident = "3")
head(c3.KO_markers, n = 10)
head(c3.Ctn_markers, n = 10)

Could "Avg_logFC" be a cause of this problem? If so, how can I get "logFC" values per sample in a cluster?

Thank you for your time and help in advance.

[Ram]

Please see How to add images to a Biostars post to add your images properly. You need the direct link to the image, not the link to the webpage that has the image embedded (which is what you have used here)

Answer 1

[swbarnes2]

If all the cells are either KO or control, then those two commands are essentially the same thing, but flip-flopping the ratios.