t-test: p=0.522656
Neutral set average density: 2.20348e-05
Different set average density: 3.03385e-05
motif_present gene_set absent present different 984 10 neutral 1942 11
Fisher's exact test: p=0.245237
Binomial GLM: p=0.182699
Call:
glm(formula = motif_present ~ different, family = binomial, data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.1422 -0.1422 -0.1063 -0.1063 3.2185
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -5.1736 0.3024 -17.110 <2e-16 ***
differentTRUE 0.5845 0.4387 1.332 0.183
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 249.50 on 2946 degrees of freedom
Residual deviance: 247.76 on 2945 degrees of freedom
AIC: 251.76
Number of Fisher Scoring iterations: 8
Binomial GLM adjusted for length: p=0.714693
Call:
glm(formula = motif_present ~ length + different, family = binomial,
data = daf)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.4770 -0.1220 -0.0960 -0.0838 3.3526
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -5.9551496 0.4100399 -14.523 < 2e-16 ***
length 0.0031360 0.0008386 3.740 0.000184 ***
differentTRUE 0.1668354 0.4563829 0.366 0.714693
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 249.50 on 2946 degrees of freedom
Residual deviance: 236.26 on 2944 degrees of freedom
AIC: 242.26
Number of Fisher Scoring iterations: 8