I would like to perform an automated paired t-test between column 2 and 3, 4 and 5, 6 and 7 and so on. When I use the code below, I am able to perform a t-test, but not an unpaired t-test.
data:
patient weight_1 weight_2 BMI_1 BMI_2 chol_1 chol_2 gly_1 gly_2
1 A 86.0 97.0 34.44961 30.61482 86.0 97.0 34.44961 30.61482
2 B 111.0 55.5 33.51045 22.80572 111.0 55.5 33.51045 22.80572
3 C 92.4 70.0 28.51852 25.71166 92.4 70.0 28.51852 25.71166
code:
names <- colnames(dataframe)
for(i in seq(from = 2, to = 8, by = 2)){
print(names[i])
print(names[i+1])
print(t.test(dataframe[i], dataframe[i+1]))
}
output:
[1] "weight_1" [1] "weight_2"
Welch Two Sample t-test
data: dataframe[i] and dataframe[i + 1]
t = 1.3183, df = 75.892, p-value = 0.1914
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
-2.459965 12.090735
sample estimates:
mean of x mean of y
91.50256 86.68718
[1] "BMI_1"
[1] "BMI_2"
Welch Two Sample t-test
data: dataframe[i] and dataframe[i + 1]
t = 1.5851, df = 75.866, p-value = 0.1171
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
-0.3817027 3.3571650
sample estimates:
mean of x mean of y
30.45167 28.96394
And so on. When I add paired=TRUE to the data:
names <- colnames(dataframe)
for(i in seq(from = 2, to = 8, by = 2)){
print(names[i])
print(names[i+1])
print(t.test(dataframe[i], dataframe[i+1]), paired=TRUE)
}
The results are exactly the same, as if it doesn't include the paired function. Could someone help me with this? Many thanks in advance.
You have to change the indexing in the t.test to define clearly that you want to use the columns:
e.g.:
df <- data.frame(a = runif(10), b=runif(10), c=runif(10))
t1 <- t.test(df[1], df[2])
t1$p.value
t2 <- t.test(df[1], df[2], paired=T)
t2$p.value
Error in `[.data.frame`(y, yok) : undefined columns selected
but
t2 <- t.test(df[,1], df[,2], paired=T)
t2$p.value
works. So in your code it should be
print(t.test(dataframe[,i], dataframe[,i+1], paired=TRUE))
for the paired t.test.
I would suggest using this form of indexing also for the paired t-test, although it does not throw any error.