Hi,
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
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