[R] How to extract x rows to get x pvalues using t.test

[Adaikalavan Ramasamy]

You will need to _apply_ the t-test row by row. 

   apply( genes, 1, function(x) t.test( x[1:2], x[3:4] )$p.value )

apply() is a C optimised version of for. Running the above code on a
dataset with 56000 rows and 4 columns took about 63 seconds on my 1.6
GHz Pentium machine with 512 Mb RAM. See help("apply") for more details.

Regards, Adai



On Tue, 2005-03-15 at 11:59 -0600, Jagarlamudi, Choudary wrote:
> Hi all,
>  
>   My data
> genes
>      [,1] [,2] [,3] [,4]
> [1,]   25   72   23   55
> [2,]   34   53   41   33
> [3,]   26   43   26   44
> [4,]   36   64   64   22
> [5,]   47   72   67   34
> 
>  stu<-t.test(genes[,1:2],genes[,3:4])
> > stu$p.value
> [1] 0.4198002
> 
> i get 1 pvalue for the entire col1:col2  Vs col3:col4. I am trying to get 5 p values for the 5 rows i have.
> I am trying to avoid a for loop coz my actual data has 56000 rows and its taking more than 4 minutes to
> compute.
>  
> Thanks in advance.
>  
> Choudary Jagarlamudi
> Instructor
> Southwestern Oklahoma State University
> STF 254
> 100 campus Drive
> Weatherford OK 73096
> Tel 580-774-7136
> 
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> 
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