I have nf-core produced ballgown folders which I successfully read in R. I followed the ballgown vignette found here.

I used pData(bg) for adding three treatment groups for 51 samples as follows:

pData(bg) = data.frame(id=sampleNames(bg), group=rep(c(rep("A",15),rep("B",20),rep("C",16))))

I performed DGE as in the vignette and after using stattest I got warning as follows the code below:

stat_results_gene = stattest(bg, feature="gene", meas="FPKM", covariate="group", getFC = TRUE)
Warning message:
In stattest(bg, feature = "gene", meas = "FPKM", covariate = "group", :
fold changes only available for 2-group comparisons

Now, I understand why I got the warning since 3-group comparison is not possible with Ballgown (realized it afterwards). I am just wondering what is the contrasts on obtained DE genes from which only p-val and q-val are reported? I have also used edgeR for this same data and obtained DGE results from there and they will be my primary results. This just bugs me where these genes are coming from.

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