Measure
Def. of p-value
C (Completeness)
A (Accuracy)
S (Combined)
Conditional
Unconditional
p (# >observed)
0.145 *
0.066 **
1/2 p (# =observed) + p(# >observed)
0.166
0.081 **
p (>= observed)
0.186
0.095 **
p (# >observed)
0.326
0.265
1/2 p (# =observed) + p(# >observed)
0.355
0.298
p (>= observed)
0.384
0.331
p (# >observed)
0.217
0.124 *
1/2 p (# =observed) + p(# >observed)
0.233
0.136 *
p (>= observed)
0.248
0.148 *
***: significant at 5% level; **: significant at 10% level; * significant at 15% level
Table 1. Simulated one-sided p-value for the hypothesis H0: the association is not stronger than expected by chance.
The observed C is 44.6%. The observed A is 64.2%. The observed S is .0076. The discussions in this
paragraph (after table 1) should be revised correspondingly.
Limiting case defined in Section
Conditional
Unconditional
2 (random selection)
4.06E-3
3.89E-3
3 (spurious genes)
1.69E-3
1.60E-3
4 (spurious QTLs)
2.37E-3
2.29E-3
2
1 (Theoretical maximum)
14.4E-3
Observed
7.58E-3
Table 2. Estimated limiting extrema of combined measure S
ni (Completeness)
mi (Accuracy)
Conditional
Unconditional
0.131 *
0.003 ***
0.624
0.508
***: significant at 5% level; **: significant at 10% level; * significant at 15% level, d.f. is 17
Table 3. p-value from the chi-square test for the hypothesis H0: the association is not different from expected by chance.
The numbers in the paragraph before table 3 should be corrected as following in red:
The p-values for our study are in Table 3. Again, they support the hypothesis that completeness is higher
than expected by chance, but accuracy is only marginally higher than expected by chance – i.e. more
genes are covered than expected, but the number of QTLs containing genes in G is about what is expected
by chance. For example, chromosome 18 and 16 have much higher positive values than average in both
completeness and accuracy (under conditional resampling and considering the contribution in
( X i - EX i )/ EX i , chromosome 18 has 3.64 in accuracy and 17.13 in completeness; chromosome 14 has
1.36 in accuracy and 2.25 in completeness; the genome average is 0.81 and 1.31 respectively), which
suggests that the genes on these two chromosomes are more likely to be associated with the drug abuse
trait, and the QTLs on these two chromosomes are more likely to be associated with the NA region than
genome-wide average.
The following table is originally for the paired tests that has been removed from the current draft. For your
information, I still updated it.
Test
C (Completeness)
A (Accuracy)
S (Combined)
Conditional
Unconditional
Paired t
0.283
0.297
Wilcoxon
0.335
0.367
Paired t
0.290
0.494
Wilcoxon
0.275
0.367
Paired t
0.272
0.245
Wilcoxon
0.305
0.351
***: significant at 5% level; **: significant at 10% level; * significant at 15% level
Table 4. p-value from the paired t and Wilcoxon signed-rank test for the hypothesis Ho: the association is not stronger than
expected by chance.