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Using the flexible cutoff a similar level of true positives was reported from all comparisons, despite the difference in size between treatment and control sets.
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D. suzukii genes are searchable using the flexible Gene Search function.
We tested the combination of the AC, Fisher's and Diff methods together with the flexible cutoff on experimental data derived from cold-stressed Arabidopsis thaliana plants, using non-stressed plants as a control.
The deciding factor seems to be the cutoff set for detecting up-regulated genes, and this has been considered in the flexible cutoff.
On the other hand, the sensitivity increases dramatically when the flexible cutoff increases and reaches to ~85% when C = 0.7.
Finally, we tested different levels for the flexible cutoff and the results can be viewed in Figure 12.
For the AC method the flexible cutoff only affects the results slightly when changing the value on C (see Fig. 9, true positives and sensitivity for AC).
The χ test introduces more false positives than the other methods when the flexible cutoff is increased from 0.3 to 0.5.
For both cold-induced EST sets the level of true positives is very low, ~25% for both sets, irrespectively of the level of the flexible cutoff.
In this case we tried the combination of 'leaving one out', i.e. all methods except one were combined with the flexible cutoff.
Referring to the example, if C = 50%, the test value cutoff will be 0.005, since the percentage number of genes with p ≤ 0.005 is 34%, which is less than C. We tested four different levels on the flexible cutoff: C = 0.1 (10%), 0.3 (30%), 0.5 (50%) and 0.7 (70%), and derived the percentage of true positives and sensitivity for each method using the same simulated data as in the above study.
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