t-test: p=0.215156
Neutral set average density: 0.00191646
Different set average density: 0.00174779
motif_present gene_set absent present different 633 361 neutral 1428 525
Fisher's exact test: p=1.67566e-07
Binomial GLM: p=1.40563e-07
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.9500 -0.7913 -0.7913 1.4233 1.6209
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.00063 0.05104 -19.605 < 2e-16 ***
differentTRUE 0.43904 0.08340 5.265 1.41e-07 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3603.6 on 2946 degrees of freedom
Residual deviance: 3576.2 on 2945 degrees of freedom
AIC: 3580.2
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.107477
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.4533 -0.7294 -0.5898 0.8097 2.0692
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -2.1122109 0.0805304 -26.23 <2e-16 ***
length 0.0053717 0.0002766 19.42 <2e-16 ***
differentTRUE -0.1559144 0.0968630 -1.61 0.107
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3603.6 on 2946 degrees of freedom
Residual deviance: 3081.7 on 2944 degrees of freedom
AIC: 3087.7
Number of Fisher Scoring iterations: 4