[R] Using perm.t.test() upon Matrix/Dataframe columns parted by factor instead of t.test()

[Gunnar Oehmichen]

Just checked. To get lapply to work for the both functions, I have to 
convert the matrix M into a dataframe. Trying it with apply for the 
matrix works perfectly fine. The missing x was the problem

So here my improved code.

require(Deducer)    #Package for perm.t.test

c(rep("A", 5), rep("B", 5))->Faktor

matrix(rnorm(100, mean=20, sd=4), nrow=10, ncol=10)->M

colnames(M) <- c("species1","species2", 
"species3","species4","species5","species6","species7","species8","species9", 
"species10")

###Conventional T-Test to test for differences of each species per factor
as.data.frame(M)->M2

apply(
   M, 2, function(x)
   t.test(x~ Faktor)
   )

lapply(
   M2,  function(x)
   t.test(x~ Faktor)
   )
#Both versions ork fine, either apply for the matrix or lapply for the 
data-frame

###Trying it for perm.t.test without the helpful formular expression

lapply(
   M2, function(x)
   perm.t.test(subset(x, Faktor=="A"),
               subset(x, Faktor=="B")))

#For the perm.t.test lapply works with a dataframe

apply(
   M, 2, function(x)
   perm.t.test(subset(x, Faktor=="A"),
               subset(x, Faktor=="B")))


Thank you very much for your help,

Gunnar
>
>
>
>> Just a hunch I can't test from my phone, but in your final lapply you 
>> are passing a function of x that has no x in it, so I wouldn't be 
>> surprised if R was unhappy about that.
>>
>> Change the latter M's to x and see if that helps.
>
> Not likely. 'x' is a formal argument of the function. He's using 
> lapply on a matrix. lapply is generally used for lists. but in this 
> case it results in sending individual numbers one-by-one to that 
> function, They are them each being t.tested against a ten item vector. 
> Failure is the predictable outcome but he did not see fit to reproduce 
> the informative error message that told him there was a mismatch of 
> lengths.
>
> He should use:
> apply(M, 2, function(x)
> t.test(x~ Faktor))