Dear all,
I have RNAseq to analyze (DE between different conditions). Mapping was done using STAR and I was planning to use edgeR for DE.
My concern is about how to proceed due to the particular design of the experiment.
I have two sets of experiments (each condition is done in triplicates, real biological triplicates).
Experiment #1:
3 conditions: Control - Treatment#1 - Treatment#2
Experiment #2:
3 conditions as well: Control - Treatment#1 - Treatment#3 (not #2 !!!)
If I analyze separately experiments 1&2, and first look at the DE genes between Treatment#1 and Control, I see some differences between both experiments. So, I did another analysis considering all the samples for Control and Treatment#1 (since then, it is like having 6 biological replicates for this Treatment).
My question is now, how do I process for Treatment#2 and #3 ? In this case, I won't have 6 replicates for each treatment (even though I will have 6 replicates for the Control and Treatment#1)? It has importance because Treatments 2 or 3 came after Treatment1 and the idea is to see the behavior of the genes affected by Treatment#1 after Treatments 2 and 3...
What is the best approach?
Thanks in advance,
s.
I have RNAseq to analyze (DE between different conditions). Mapping was done using STAR and I was planning to use edgeR for DE.
My concern is about how to proceed due to the particular design of the experiment.
I have two sets of experiments (each condition is done in triplicates, real biological triplicates).
Experiment #1:
3 conditions: Control - Treatment#1 - Treatment#2
Experiment #2:
3 conditions as well: Control - Treatment#1 - Treatment#3 (not #2 !!!)
If I analyze separately experiments 1&2, and first look at the DE genes between Treatment#1 and Control, I see some differences between both experiments. So, I did another analysis considering all the samples for Control and Treatment#1 (since then, it is like having 6 biological replicates for this Treatment).
My question is now, how do I process for Treatment#2 and #3 ? In this case, I won't have 6 replicates for each treatment (even though I will have 6 replicates for the Control and Treatment#1)? It has importance because Treatments 2 or 3 came after Treatment1 and the idea is to see the behavior of the genes affected by Treatment#1 after Treatments 2 and 3...
What is the best approach?
Thanks in advance,
s.
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