Entering edit mode
2.6 years ago
shome
▴
10
I have performed differential expression analysis on my dataset using the Scanpy package and Wilcoxon-rank sum testing.To carry out the same, I used the following tutorial link :
https://nbisweden.github.io/workshop-scRNAseq/labs/compiled/scanpy/scanpy_05_dge.html
Now, my issue is I don't see a very big difference in expression values for the DE genes when I plot them, particularly comparing between control and conditions. How to make sure which DE genes fall under statistically significant criteria?
I used the following code :
to get the adjusted p-values and logFC,which is as follows :
Generally p-value < 0.01 is considered statistically significant.But, in my case, all the genes in the dataset are having p-value < 0.01, which is making me confused about whether I have approached it appropriately.