Group-specific treatment effect
0
Entering edit mode
L_K • 0
@l_k-14850
Last seen 21 days ago

Hey everybody.

I do have a project with the exact same design as in the DESEQ2 manual under "Group-specific condition effect". Meaning I have two groups of diseased animals, one group treated with drug 1 (2 timepoints: baseline and treated) and one group treated with drug2 (different individuals in each group).

So I was pretty much following the manual, however the whole thing is quite complex for my limited understanding.

My main question is how to phrase it what the differentially expressed genes represent?

my results() call looks as follows: resGroup<-results(dds, contrast=list("TreatmentDrug2.Timepointtreated","TreatmentDrug1.Timepointtreated"))

Is this reasonable? And how would I describe what the diff. expressed genes represent? What about something along the lines of: Genes that are responding differently to the two treatments, taking into account the intra-individual effect? (And would a log2fold change of +2 mean that the expression is accordingly higher in drug2 compared to drug1; taking into account effect of individuals)?

Thanks a lot and merry christmas!

DESeq2 differentialexpressionanalysis • 80 views
ADD COMMENTlink
0
Entering edit mode
@mikelove
Last seen 2 days ago
United States

Due to limited time, I can only offer software related support here. A lot of users also require assistance interpreting results, but I unfortunately don't have time to provide this type of consultation on the support site. I'd recommend to collaborate with a statistician local to your institute to help with interpretation of design and contrasts.

ADD COMMENTlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Help About
FAQ
Access RSS
API
Stats

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

Powered by the version 2.3.3