Hi,

I am trying to understand the ballgown output for differential expression analysis.

I see only positive values in the fold changes. From the earlier posts, I found that FC<1 indicates down regulation and FC>1 indicates upregulation. In my case, I used 2-group comparisons where the labels were control and inoculated and in another category, it was resistant vs moderately resistant. So I am not sure which will be considered as the reference category???

Like, if FC>1 indicates upregulation in the inoculated group? or is it the other way around??

Any advice on this will be greatly appreciated.

Many thanks

-Amy