t-test: p=0.408327
Neutral set average density: 7.49124e-05
Different set average density: 5.57969e-05
motif_present gene_set absent present different 971 23 neutral 1923 30
Fisher's exact test: p=0.14347
Binomial GLM: p=0.135742
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.2164 -0.2164 -0.1760 -0.1760 2.8900
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -4.1604 0.1840 -22.612 <2e-16 ***
differentTRUE 0.4176 0.2799 1.492 0.136
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 530.98 on 2946 degrees of freedom
Residual deviance: 528.80 on 2945 degrees of freedom
AIC: 532.8
Number of Fisher Scoring iterations: 7
Binomial GLM adjusted for length: p=0.848731
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.8035 -0.1876 -0.1475 -0.1303 3.1472
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -5.0732853 0.2611908 -19.424 < 2e-16 ***
length 0.0035561 0.0005322 6.682 2.36e-11 ***
differentTRUE -0.0559105 0.2931266 -0.191 0.849
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 530.98 on 2946 degrees of freedom
Residual deviance: 491.36 on 2944 degrees of freedom
AIC: 497.36
Number of Fisher Scoring iterations: 7