I've just started using R and fdrtool, and I'm not sure if the qvalues I'm receiving back are accurate. I performed fdrtool on pvalues obtained from a two way anova on proteomics data. So I have 266 data values (protein spots) for two factors (ft, vr, and the interaction) for each biological sample.
One of the two factors (vr) has a highly significant effect with 119 protein spots significantly affected at p<0.05. When I run the fdrtool, the qvalues are slightly higher than pvalues (as expected), but only up to p<0.01. Between p<0.01 and p<0.05, the qvalues are lower, giving me more significant protein spots at that level - is this correct?
The other factor (ft) had only 3 weakly significant protein spots. When I run fdrtool, all 266 qvalues are 1.
The interaction effect (ftxvr) produced 14 significant pvalues (mostly p<0.05, a couple are p<0.01). fdrtool produces qvalues ranging between 0.87-0.99 and the rise with rising pvalues, so I lose the significant results here.
Best wishes, Catherine
Mmmm, I am not sure, but I would expect that q-values should be >= p-values, always. Maybe you can post some small example dataset giving "strange" results. Also, you could try using p.adjust. It always worked well for me.