Question

I have a problem using data from a tab delimited data file imported with read.delim.

Most of the columns contain numerical data which I need to do a t.test for. Unfortunately I always get this error:

Error in if (stderr < 10 * .Machine$double.eps * max(abs(mx), abs(my))) 
            stop("data are essentiallyconstant") :
missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In mean.default(x) : argument is not numeric or logical: returning NA
2: In mean.default(y) : argument is not numeric or logical: returning NA

I noticed that this only happens with vectors that consist of different levels.
It won’t even perform simple numerical operations like vector[1] + vector[2] for leveled vectors.
Vectors without levels work fine, though.

How can I use the data in the leveled vectors for calculation?

Thank you

Answer 1

I have been able to reproduce your error message with the following small example:

x = as.factor(1:5)
y = as.factor(1:5)

t.test(x, y)

yields

Error in if (stderr < 10 * .Machine$double.eps * max(abs(mx), abs(my))) stop("data are essentially constant") : 
  missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In mean.default(x) : argument is not numeric or logical: returning NA
2: In mean.default(y) : argument is not numeric or logical: returning NA

The problem is you are trying to perform a t-test on non-numeric vectors. Addition likewise is not defined for factors:

x + y

yields

[1] NA NA NA NA NA
Warning message:
In Ops.factor(x, y) : + not meaningful for factors

The warning gives keen insight as to what is amiss and also explains why your t-test is not working.

To fix the problem, you need to do as ilya suggests: convert your vectors to numeric with as.numeric(as.character())