I have some RNA seq data with 3 genotypes and two treatments. I'd like to do pairwise comparisons between every group. Is there an easy way to do this in ballgown, or do I need to subset my dataset into each combination of genotype/treatment, and run the ballgown pipeline on them pair by pair? What I really want as an output is a table of log2 fold change values for each pairwise comparison.
The command where I think this may be relevent is pasted below:
> results_transcripts = stattest(bg_chrX_filt, feature="transcript", covariate="genotype_salt_mM", getFC=TRUE, meas="FPKM")
In stattest(bg_chrX_filt, feature = "transcript", covariate = "genotype_salt_mM", :
fold changes only available for 2-group comparisons