Ravi_HMW_v2
Dihua Xu
May 22, 2017
Compare difference between two dataset
## Phenotype
## Group 0 1
## Case 37 42
## Control 52 0## # A tibble: 37 × 6
## `Sample ID` `MOMS ID` Phenotype Group `Adiponectin, ng/ml` Adiponectin
## <dbl> <dbl> <dbl> <fctr> <dbl> <dbl>
## 1 2452 2452 0 Case 14906.220 14906.220
## 2 3238 3238 0 Case 6650.462 6650.462
## 3 3388 3388 0 Case 12484.690 12484.690
## 4 3792 3792 0 Case 6631.100 6631.100
## 5 4185 4185 0 Case 11015.030 11015.030
## 6 4316 4316 0 Case 3592.253 3592.253
## 7 4447 4447 0 Case 13855.400 13855.400
## 8 5217 5217 0 Case 7996.852 7996.852
## 9 5345 5345 0 Case 15651.600 15651.600
## 10 5844 5844 0 Case 6379.809 6379.809
## 11 5974 5974 0 Case 6408.764 6408.764
## 12 6186 6186 0 Case 4635.291 4635.291
## 13 6690 6690 0 Case 9351.868 9351.868
## 14 6965 6965 0 Case 13076.570 13076.570
## 15 7036 7036 0 Case 20752.940 20752.940
## 16 7245 7245 0 Case 8786.037 8786.037
## 17 7789 7789 0 Case 3435.894 3435.894
## 18 7945 7945 0 Case 1820.852 1820.852
## 19 8225 8225 0 Case 16848.050 16848.050
## 20 8408 8408 0 Case 6941.431 6941.431
## 21 8666 8666 0 Case 11055.370 11055.370
## 22 8827 8827 0 Case 10672.630 10672.630
## 23 8912 8912 0 Case 7067.828 7067.828
## 24 9033 9033 0 Case 15713.840 15713.840
## 25 9035 9035 0 Case 2492.700 2492.700
## 26 9052 9052 0 Case 8865.281 8865.281
## 27 9248 9248 0 Case 15994.200 15994.200
## 28 9768 9768 0 Case 8607.954 8607.954
## 29 10049 10049 0 Case 20191.170 20191.170
## 30 10102 10102 0 Case 12902.850 12902.850
## 31 10127 10127 0 Case 13015.240 13015.240
## 32 340 340 0 Case 4008.747 4008.747
## 33 1004 1004 0 Case 21103.330 21103.330
## 34 1427 1427 0 Case 18376.890 18376.890
## 35 679 679 0 Case 2934.058 2934.058
## 36 8605 8605 0 Case 6004.371 6004.371
## 37 7921 7921 0 Case 7409.022 7409.022Analyses based on Case/Control status
##
## Shapiro-Wilk normality test
##
## data: dat$Adiponectin
## W = 0.97262, p-value = 0.009439##
## Welch Two Sample t-test
##
## data: Adiponectin by Group
## t = -1.613, df = 116.47, p-value = 0.1095
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## -3289.3102 336.4595
## sample estimates:
## mean in group Case mean in group Control
## 9336.351 10812.777##
## Wilcoxon rank sum test with continuity correction
##
## data: Adiponectin by Group
## W = 1688.5, p-value = 0.08597
## alternative hypothesis: true location shift is not equal to 0P value from Shapiro-Wilk normality test is 0.0094. Suggesting Wilcoxon test might be more appropriate. P value from Wilcox test is 0.086; Suggesting bordline significance between case and control.
##
## Call:
## lm(formula = Adiponectin ~ Group + `GA in weeks`, data = dat)
##
## Residuals:
## Min 1Q Median 3Q Max
## -9135 -3490 -1125 3764 13193
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 4519.9 3740.3 1.208 0.229
## GroupControl 1413.1 932.7 1.515 0.132
## `GA in weeks` 442.2 339.2 1.304 0.195
##
## Residual standard error: 5216 on 128 degrees of freedom
## Multiple R-squared: 0.03186, Adjusted R-squared: 0.01674
## F-statistic: 2.106 on 2 and 128 DF, p-value: 0.1259##
## Call:
## lm(formula = Adiponectin ~ Group + bmi, data = dat)
##
## Residuals:
## Min 1Q Median 3Q Max
## -10730.6 -3327.3 -490.5 3581.0 11470.6
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 19640.7 2871.6 6.840 2.93e-10 ***
## GroupControl 495.4 931.5 0.532 0.595734
## bmi -390.0 106.6 -3.659 0.000369 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 4996 on 128 degrees of freedom
## Multiple R-squared: 0.1119, Adjusted R-squared: 0.09803
## F-statistic: 8.064 on 2 and 128 DF, p-value: 0.0005029##
## Call:
## lm(formula = Adiponectin ~ Group + `GA in weeks` + bmi, data = dat)
##
## Residuals:
## Min 1Q Median 3Q Max
## -10151.9 -3442.8 -984.1 3497.4 12063.9
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 15238.1 4648.6 3.278 0.001349 **
## GroupControl 453.7 930.5 0.488 0.626678
## `GA in weeks` 390.5 324.6 1.203 0.231202
## bmi -384.3 106.5 -3.609 0.000441 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 4987 on 127 degrees of freedom
## Multiple R-squared: 0.1219, Adjusted R-squared: 0.1012
## F-statistic: 5.877 on 3 and 127 DF, p-value: 0.0008642After adjusting for BMI and/or Gastational age, the group effect becomes non-significant.
Analyses based on Phenotype
##
## Shapiro-Wilk normality test
##
## data: dat$Adiponectin
## W = 0.97262, p-value = 0.009439##
## Welch Two Sample t-test
##
## data: Adiponectin by factor(Phenotype)
## t = 2.0083, df = 76.821, p-value = 0.04813
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## 16.82847 3964.77211
## sample estimates:
## mean in group 0 mean in group 1
## 10560.685 8569.885##
## Wilcoxon rank sum test with continuity correction
##
## data: Adiponectin by factor(Phenotype)
## W = 2291.5, p-value = 0.03742
## alternative hypothesis: true location shift is not equal to 0P values from both tests are < 0.05.
##
## Call:
## lm(formula = Adiponectin ~ factor(Phenotype) + `GA in weeks`,
## data = dat)
##
## Residuals:
## Min 1Q Median 3Q Max
## -8758.4 -4071.2 -906.5 3685.9 13487.6
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 6271.1 3800.3 1.650 0.1014
## factor(Phenotype)1 -1849.1 979.6 -1.888 0.0614 .
## `GA in weeks` 387.7 339.8 1.141 0.2561
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 5191 on 128 degrees of freedom
## Multiple R-squared: 0.04119, Adjusted R-squared: 0.02621
## F-statistic: 2.749 on 2 and 128 DF, p-value: 0.06775##
## Call:
## lm(formula = Adiponectin ~ factor(Phenotype) + bmi, data = dat)
##
## Residuals:
## Min 1Q Median 3Q Max
## -10758.7 -3550.2 -530.8 3443.1 11720.5
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 19888.0 2633.1 7.553 7.09e-12 ***
## factor(Phenotype)1 -1221.4 954.3 -1.280 0.20292
## bmi -376.6 104.2 -3.615 0.00043 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 4969 on 128 degrees of freedom
## Multiple R-squared: 0.1212, Adjusted R-squared: 0.1075
## F-statistic: 8.825 on 2 and 128 DF, p-value: 0.0002567##
## Call:
## lm(formula = Adiponectin ~ factor(Phenotype) + `GA in weeks` +
## bmi, data = dat)
##
## Residuals:
## Min 1Q Median 3Q Max
## -10227.8 -3356.5 -556.6 3308.7 12537.1
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 15900.7 4520.9 3.517 0.000606 ***
## factor(Phenotype)1 -1099.3 960.3 -1.145 0.254454
## `GA in weeks` 352.8 325.3 1.085 0.280159
## bmi -373.2 104.1 -3.584 0.000481 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 4966 on 127 degrees of freedom
## Multiple R-squared: 0.1293, Adjusted R-squared: 0.1087
## F-statistic: 6.284 on 3 and 127 DF, p-value: 0.0005205After adjusting for BMI and/or Gastational age, the Phenotype effect becomes non-significant.