R help - Mar 2007 - Row-wise two sample T-test on subsets of a matrix

Hello all,

I am trying to run a two sample t-test on a matrix which is a
196002*22 matrix. I want to run the t-test, row-wise, with the
first 11 columns being a part of the first group and columns
12-22 being a part of the second group. 

I tried running something like (temp.matrix being my 196002*22
matrix)

t.test(temp.matrix[,1:11],temp.matrix[,12:22],paired=TRUE)

or somthing like

as.numeric(t.test(temp.matrix[,1:11],temp.matrix[,12:22],paired=TRUE)[[1]])
so as to only capture the t-value alone and 

and I get a result for the whole matrix instead of a row-wise
result. 

I want to avoid using a "for" loop to increment the number of
rows as it would take a huge amount of time.


Any suggestions would be really appreciated.

thanks
nameeta

Here's one suggestion: convert the matrix into a three-dimensional array and
use apply on it.

Ranjan

On Thu,  1 Mar 2007 11:51:29 -0600 (CST) Nameeta Lobo <nlobo at
uchicago.edu> wrote:
> Hello all,
> 
> I am trying to run a two sample t-test on a matrix which is a
> 196002*22 matrix. I want to run the t-test, row-wise, with the
> first 11 columns being a part of the first group and columns
> 12-22 being a part of the second group. 
> 
> I tried running something like (temp.matrix being my 196002*22
> matrix)
> 
> t.test(temp.matrix[,1:11],temp.matrix[,12:22],paired=TRUE)
> 
> or somthing like
> 
> as.numeric(t.test(temp.matrix[,1:11],temp.matrix[,12:22],paired=TRUE)[[1]])
> so as to only capture the t-value alone and 
> 
> and I get a result for the whole matrix instead of a row-wise
> result. 
> 
> I want to avoid using a "for" loop to increment the number of
> rows as it would take a huge amount of time.
> 
> 
> Any suggestions would be really appreciated.
> 
> thanks
> nameeta
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
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> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

This is the kind of thing that rowMeans was made for.
For the numerator of the t statistic:

x1 <- temp.matrix[,1:11]
x2 <- temp.matrix[,12:22]
numerator <- rowMeans(x1) - rowMeans(x2)

For the denominator, if you're using S+ you can use rowVars;
in R you can program a simple version quickly, e.g.

rowVars <- function(x){
  means <- rowMeans(x)
  rowSums((x - means)^2) / (ncol(x)-1)
}

Tim Hesterberg
>Hello all,
>
>I am trying to run a two sample t-test on a matrix which is a
>196002*22 matrix. I want to run the t-test, row-wise, with the
>first 11 columns being a part of the first group and columns
>12-22 being a part of the second group. 
>
>I tried running something like (temp.matrix being my 196002*22
>matrix)
>
>t.test(temp.matrix[,1:11],temp.matrix[,12:22],paired=TRUE)
>
>or somthing like
>
>as.numeric(t.test(temp.matrix[,1:11],temp.matrix[,12:22],paired=TRUE)[[1]])
>so as to only capture the t-value alone and 
>
>and I get a result for the whole matrix instead of a row-wise
>result. 
>
>I want to avoid using a "for" loop to increment the number of
>rows as it would take a huge amount of time.
>
>
>Any suggestions would be really appreciated.
>
>thanks
>nameeta
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