RNA-Seq DEG analysis questions
1
0
Entering edit mode
mullin.yu • 0
@mullinyu-13995
Last seen 4.1 years ago

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!

rnaseq deg • 723 views
ADD COMMENT
0
Entering edit mode
@gordon-smyth
Last seen 1 hour ago
WEHI, Melbourne, Australia

My advice would be to analyse the blood samples and the fibroblast samples separately. Then the comparison of the proband with the control samples is a simple two-group comparison (n=1 proband vs n=3 controls). Any of the usual packages limma, edgeR or DESeq2 would be able to do the DE analysis easily.

ADD COMMENT

Login before adding your answer.

Traffic: 140 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6