t-test: p=0.416883
Neutral set average density: 1.74493e-05
Different set average density: 2.71946e-05
motif_present gene_set absent present different 985 9 neutral 1944 9
Fisher's exact test: p=0.208891
Binomial GLM: p=0.150642
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.1349 -0.1349 -0.0961 -0.0961 3.2802
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -5.3753 0.3341 -16.089 <2e-16 ***
differentTRUE 0.6799 0.4730 1.437 0.151
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 219.42 on 2946 degrees of freedom
Residual deviance: 217.40 on 2945 degrees of freedom
AIC: 221.4
Number of Fisher Scoring iterations: 8
Binomial GLM adjusted for length: p=0.599215
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.4573 -0.1127 -0.0884 -0.0757 3.4140
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -6.166282 0.448943 -13.735 < 2e-16 ***
length 0.003162 0.000901 3.509 0.00045 ***
differentTRUE 0.258453 0.491794 0.526 0.59921
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 219.42 on 2946 degrees of freedom
Residual deviance: 207.27 on 2944 degrees of freedom
AIC: 213.27
Number of Fisher Scoring iterations: 8