Ballgown
Hello
I have following samples:
- Wt-treatment1
- Wt-treatment2
- mutant1-treatment1
- mutant1-treatment2
- mutant2-treatment1
- mutant2-treatment2
And for each of these six different samples, three replicate are present. How do I mention to ballgown (for performing Differential expression analysis) to take into account triplicates of each sample. For example if I want to compare the genes between Wt-treatment1 and Wt-treatment2, comparison should be made between the average of triplicates of these to samples. How do I mention that in stattest command of ballgown package?
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What have you tried? What does the object you pass to
stattestlook like?