Currently, I have the following RNA samples and want to see any up/down-regulated gene expression in proband to explain the disease-causing of the proband.
Sample1: (Proband) blood
Sample2: (Proband) fibroblast
Sample3: (Control person #1) blood
Sample4: (Control person #1) fibroblast
Sample5: (Control person #2) blood
Sample6: (Control person #2) fibroblast
Sample7: (Control person #3) blood
Sample8: (Control person #3) fibroblast
In this case,
1. Can I do the DEG? Any tool would be better in this case (DESeq/edgeR)
2. Can I treat control samples as biological replica of proband? If not, I know edgeR has a section to deal with the case without replica
3. Is it statistically significant? And any way to improve in a better setting?
Thanks a lot!