I have the following dataframe I'm calling "test" and I am trying to run a Bartlett's test and a Kruskal-Wallis test for each "metab" vs the "diagnosis"
> test
Index tube.label age gender diagnosis metab1 metab2 metab3 metab4 metab5 metab6
1 200 73 Male Cancer 6 1.5 2 5 8 1.5
2 201 71 Male Healthy 6 1.5 2 11.5 50 1.5
4 202 76 Male Adenoma 2 1.5 2 5 8 1.5
7 203 58 Female Cancer 2 1.5 2 1.5 2.5 1.5
9 204 73 Male Cancer 2 1.5 2 1.5 8 1.5
12 205 72 Male Healthy 6 1.5 17.8272 13.5 184.2 4.5
13 206 46 Female Cancer 30.0530 1.5 2 21.2 16.6 4.5
14 207 38 Female Healthy 6 1.5 2 12.494 31.59 1.5
15 208 60 Male Cancer 6 1.5 2 13.2 53.2 4.5
16 209 72 Female Cancer 6 1.5 2 1.5 8 1.5
17 210 72 Male Adenoma 6 1.5 2 22.829 102.44 9.069
18 211 52 Male Cancer 6 1.5 2 1.5 8 1.5
19 212 64 Male Healthy 6 1.5 2 1.5 8 1.5
20 213 68 Male Cancer 6 1.5 2 26.685 40.9 4.5
21 214 60 Male Healthy 24.902 1.5 42.443 22.942 498.5 4.5
23 215 70 Female Healthy 6 1.5 2 1.5 19.908 4.5
24 216 42 Female Healthy 6 1.5 2 1.5 17.7 1.5
25 217 72 Male Inflammation 6 1.5 2 1.5 8 1.5
26 218 71 Male Healthy 51 1.5 2 41.062 182.2 11.340
27 219 51 Female Inflammation 2 1.5 2 1.5 8 1.5
I can run them individually and it gives me the proper value:
bartlett.test(metab1 ~ diagnosis, data = test)
Bartlett test of homogeneity of variances
data: metab1 by diagnosis
Bartlett's K-squared = 5.1526, df = 3, p-value = 0.161
kruskal.test(metab1 ~ diagnosis, data = test)
Kruskal-Wallis rank sum test
data: metab1 by diagnosis
Kruskal-Wallis chi-squared = 4.3475, df = 3, p-value = 0.2263
However when I try to run a for loop (I have more than 100 of them to run) I keep getting the following error:
Bartlett error:
testcols <- colnames(test[6:ncol(test)])
for (met in testcols){
bartlett.test(met ~ diagnosis, data = test)
}
>Error in model.frame.default(formula = met ~ diagnosis, data = test) :
variable lengths differ (found for 'diagnosis')
Kruskal-Wallis error:
for(met in testcols){
kruskal.test(met ~ diagnosis,data = test)
}
>Error in model.frame.default(formula = met ~ diagnosis, data = test) :
variable lengths differ (found for 'diagnosis')
Should I be using something else? Thank you for the help!
Try to create formula to apply using reformulate :
cols <- names(test)[6:ncol(test)]
all_test <- lapply(cols, function(x)
bartlett.test(reformulate("diagnosis", x), data = test))
You can do the same with kruskal.test.