Hello! I am new to bioinformatics, and I would really appreciate someone's help. I have a question regarding the calculation of the significance of overlap on the Venn diagram. Let's say for two samples group(three samples in each group), I have a number of DEGs:
#### Sample_Group_KO_plus_1_vs_Pos
## out of 21852 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 3028, 14%
## LFC < 0 (down) : 3318, 15%
## outliers [1] : 26, 0.12%
## low counts [2] : 5928, 27%
## (mean count < 1)
#### Sample_Group_KO_plus_2_vs_Pos
##
## out of 21852 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up) : 3038, 14%
## LFC < 0 (down) : 3224, 15%
## outliers [1] : 26, 0.12%
## low counts [2] : 5928, 27%
## (mean count < 1)
From those two samples, I have filtered out significantly DEGs based on criteria: abs(LFC) >= 1 and p.adj < 0.1
For sample KO_plus_1_vs_Pos:702
For sample KO_plus_2_vs_Pos:1118
Now I used the fisher test to calculate the significance:
fisher.test(matrix(c(11135,175,591,527),nrow=2),alternative="greater")
527 - Number of overlapped significant DE genes between two samples KO_plus_1 and KO_plus_2
175 - Unique significant DE genes for sample KO_plus_1_vs_Pos
591 - Unique significant DE genes for sample KO_plus_2_vs_Pos
11135 - the sum of DEGs from sample KO_plus_1 and KO_plus_2 subtracted by the sum of intersected genes + unique genes (527+175+591).
Is my solution correct? Thank you very much for your help!
