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...ected), 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 [[alternative HTML version deleted]]