t-test: p=0.00123367
Neutral set average density: 0.00431055
Different set average density: 0.00499438
motif_present gene_set absent present different 296 698 neutral 1025 928
Fisher's exact test: p=2.97917e-32
Binomial GLM: p=7.02739e-31
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.5565 -1.1355 0.8408 1.2199 1.2199
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.09942 0.04531 -2.194 0.0282 *
differentTRUE 0.95728 0.08285 11.554 <2e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 4053.8 on 2946 degrees of freedom
Residual deviance: 3913.3 on 2945 degrees of freedom
AIC: 3917.3
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.0220662
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.3979 -0.8755 0.1770 0.9265 1.8005
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.6599903 0.0835527 -19.868 <2e-16 ***
length 0.0092642 0.0004439 20.871 <2e-16 ***
differentTRUE 0.2261053 0.0987693 2.289 0.0221 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 4053.8 on 2946 degrees of freedom
Residual deviance: 3131.4 on 2944 degrees of freedom
AIC: 3137.4
Number of Fisher Scoring iterations: 5