Entering edit mode
This is an RNAseq experiment where I'm trying figure out how to setup the contrast and I can't seem to figure it out. I have 3 groups.
- ( Normal FGFR1, Normal ACO2 ) - ( High FGFR1, Normal ACO2 ) ==> this comparison will give me all FGFR1 dependent genes.
- ( High FGFR1, Normal ACO2 ) - ( High FGFR1, low ACO2 ) ==> this comparison will give me all ACO2 dependent gene in the presence of high FGFR1
the issue is I also want is to find ACO2 dependent genes in the presence of normal FGFR1 as well. However, I do not have a ( Normal FGFR1, low ACO2) group.
Thus the question: is there way to set up a contrast between the 3 groups to answer this? ACO2 dependent genes in the presence of normal FGFR1.
For example, would this contrast address this?
( Normal FGFR1, Normal ACO2 + High FGFR1, Normal ACO2 ) /2 - ( High FGFR1, low ACO2 )
Gordon Smyth ok thank you for taking the time to answer the rest of question on this forum though; much appreciated.
I can add one comment. The contrast you propose does just what is appears to do, and you can see that it will give you some FGFR1 effect as well as the ACO2 effect. Only you make the judgement as to whether that is useful for your purposes. Obviously a contrast can't make up entirely for a missing experimental group.