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

From: Liaw, Andy <andy_liaw_at_merck.com>
Date: Wed 16 Mar 2005 - 11:43:26 EST


> From: 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.

That's not true. In R, there's a for loop hidden inside apply() (just look at the source). In S-PLUS, C level looping is done in some situations, and for others lapply() is used.

Andy  

> 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
> >
> > [[alternative HTML version deleted]]
> >
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R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Wed Mar 16 11:48:46 2005

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