Hi,

I would like to do three group comparison using Ballgown... When I do, I get the following warning message. I am not sure if it had calculated the differential expression based on the three groups, because this is just a warning message. If not, can you please suggest me on what code I should be using under the given circumstance?

Many thanks!!!!

> result_gene01_prr22=stattest(bgfilt_t22, feature="gene", covariate="genotype", getFC=TRUE, meas="FPKM")
Warning message:
In stattest(bgfilt_t22, feature = "gene", covariate = "genotype",  :  fold changes only available for 2-group comparisons