Need help to perform an automated unpaired t-test over different columns from CSV document in R-CodePudding

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 and 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:

> 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:
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]), paired=TRUE)
  }

the results are exactly the same, as if he doesn't included the paired function.
Could someone help me with this?
Many thanks in advance

CodePudding user response：

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 through any error.