t-test: p=0.801017
Neutral set average density: 2.09496e-05
Different set average density: 2.50487e-05
motif_present gene_set absent present different 985 9 neutral 1948 5
Fisher's exact test: p=0.0217787
Binomial GLM: p=0.0231473
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.1349 -0.1349 -0.0716 -0.0716 3.4548
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -5.9651 0.4477 -13.323 <2e-16 ***
differentTRUE 1.2697 0.5591 2.271 0.0231 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 177.72 on 2946 degrees of freedom
Residual deviance: 172.26 on 2945 degrees of freedom
AIC: 176.26
Number of Fisher Scoring iterations: 8
Binomial GLM adjusted for length: p=0.130177
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.4304 -0.1049 -0.0701 -0.0576 3.6238
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -6.69853 0.55753 -12.015 < 2e-16 ***
length 0.00298 0.00103 2.893 0.00381 **
differentTRUE 0.87584 0.57872 1.513 0.13018
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 177.72 on 2946 degrees of freedom
Residual deviance: 165.29 on 2944 degrees of freedom
AIC: 171.29
Number of Fisher Scoring iterations: 8