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Seurat FindMarkers() output interpretation

Bioinformatics Asked on October 3, 2021

FeaturePlot of the first four featuresI am using FindMarkers() between 2 groups of cells, my results are listed but i’m having hard time in choosing the right markers. Do I choose according to both the p-values or just one of them? If one of them is good enough, which one should I prefer? I am interested in the marker-genes that are differentiating the groups, so what are the parameters i should look for?

             p_val avg_logFC pct.1 pct.2  p_val_adj
UBD   3.080608e-06 1.7755753     1 0.000 0.07683959
CFB   1.262305e-05 1.3989233     1 0.067 0.31485675
RGS13 1.548593e-05 0.9009480     1 0.200 0.38626551
PYDC1 1.896309e-05 0.9622537     1 0.133 0.47299636
BIRC3 4.099414e-05 1.0129472     1 1.000 1.00000000
ICAM1 4.379895e-05 0.8219610     1 0.200 1.00000000

as you can see, p-value seems significant, however the adjusted p-value is not. and when i performed the test i got this warning In wilcox.test.default(x = c(BC03LN_05 = 0.249819542916203, ... : cannot compute exact p-value with ties
I am completely new to this field, and more importantly to mathematics. Please help me understand in an easy way.

One Answer

The p-values are not very very significant, so the adj. p-value. You need to plot the gene counts and see why it is the case. It could be because they are captured/expressed only in very very few cells. VlnPlot or FeaturePlot functions should help. You haven't shown the TSNE/UMAP plots of the two clusters, so its hard to comment more.

Answered by geek_y on October 3, 2021

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