Upon comparing my results for the analysis between DESeq2 and EdgeR, I have realized that the 2 results obtained after DEG analysis are extremely different from each other. The thresholds I have set for upregulated genes are Padj < 0.05 and log2FC >0 and log2FC <0 for downregulated genes. I understand that both are different packages and hence can yield different results which have been mentioned in another post. However, there seems to be something more concerning in the 2 results I have obtained.
- Out of all the genes reported to be upregulated in both packages; 30% are common between the 2 packages (EdgeR and DESeq2)
- Conversely, when comparing genes reported to be upregulated in DESeq2 and reported to be downregulated in EdgeR, there is also a 30% overlap. In this case the 100% constitutes the total number of genes reported to be upregulated in DESeq2 and downregulated in EdgeR.
I am not sure what I could have done wrong. I have also ensured that I releveled both reference conditions to the control.