t-test: p=0.00117731
Neutral set average density: 0.0015997
Different set average density: 0.0020396
motif_present gene_set absent present different 601 393 neutral 1468 485
Fisher's exact test: p=4.35269e-16
Binomial GLM: p=2.64455e-16
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-1.0031 -0.7556 -0.7556 1.3623 1.6691
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.10751 0.05237 -21.146 < 2e-16 ***
differentTRUE 0.68272 0.08338 8.189 2.64e-16 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3590.0 on 2946 degrees of freedom
Residual deviance: 3523.4 on 2945 degrees of freedom
AIC: 3527.4
Number of Fisher Scoring iterations: 4
Binomial GLM adjusted for length: p=0.557156
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.7603 -0.6842 -0.5293 0.6779 2.1382
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -2.4438039 0.0875955 -27.899 <2e-16 ***
length 0.0063123 0.0003002 21.029 <2e-16 ***
differentTRUE 0.0577434 0.0983585 0.587 0.557
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 3590.0 on 2946 degrees of freedom
Residual deviance: 2899.7 on 2944 degrees of freedom
AIC: 2905.7
Number of Fisher Scoring iterations: 4