I have an OTU relative abundance table with 6 treatments including the control. When I input the OTU file with all treatments I get an LDA plot with all treatments listed. When I made separate OTU tables with one specific treatment and the control, I get an entirely different LDA score plot with new features listed along with negative LDA scores (the one with all treatments had positive scores). Which way is most appropriate when I want to compare differences between a specific treatment and the control class? What is causing these differences? Is the first plot comparing all classes with one another?