R help - May 2013 - How to repeat 2 functions in succession for 400 times? (microarray data)

Hi,
May be this helps:

?set.seed(24)
?mydata4<- as.data.frame(matrix(sample(1:100,10*38,replace=TRUE),ncol=38)) 
?dim(mydata4)
#[1] 10 38
?library(matrixStats)
res<-do.call(cbind,lapply(1:400, function(i)
{permutation<-sample(mydata4);
(rowMeans(permutation[,1:27])-rowMeans(permutation[,28:38]))/(rowSds(permutation[,1:27])+rowSds(permutation[,28:38]))}
))
?dim(res)
#[1]? 10 400


A.K.
>I want to do permutation test and then get a PGC score 400 times on mydata4
(microarray data)
>
>I use 2 functions as below: 
>1. permutation<-sample(mydata4) 
>2. PGC <- (rowMeans(permutation[ ,1:27]) - rowMeans(permutation[ 
,28:38]))/ (rowSds(permutation [,1:27]) + rowSds(permutation [,28:38]))
>
>What should I do to repeat these 2 functions in succession for 
400 times and combine (cbind?) the 400 PGC score for the 7129 genes in 
one file? 
>
>Can any one help, thanks!

On May 11, 2013, at 9:21 AM, arun wrote:
> Hi,
> May be this helps:
> 
>  set.seed(24)
>  mydata4<-
as.data.frame(matrix(sample(1:100,10*38,replace=TRUE),ncol=38))
>  dim(mydata4)
> #[1] 10 38
>  library(matrixStats)
> res<-do.call(cbind,lapply(1:400, function(i)
{permutation<-sample(mydata4);
(rowMeans(permutation[,1:27])-rowMeans(permutation[,28:38]))/(rowSds(permutation[,1:27])+rowSds(permutation[,28:38]))}
))
>  dim(res)
> #[1]  10 400
> 
> 
> A.K.
> 
>> I want to do permutation test and then get a PGC score 400 times on
mydata4 (microarray data)
>> 
>> I use 2 functions as below: 
>> 1. permutation<-sample(mydata4) 
>> 2. PGC <- (rowMeans(permutation[ ,1:27]) - rowMeans(permutation[ 
> ,28:38]))/ (rowSds(permutation [,1:27]) + rowSds(permutation [,28:38])) 
>> 
>> What should I do to repeat these 2 functions in succession for 
> 400 times and combine (cbind?) the 400 PGC score for the 7129 genes in 
> one file? 
Couldn't that just be:

fourPGCs <- replicate(400, {  permutation<-sample(mydata4) 
 PGC <- (rowMeans(permutation[ ,1:27]) - 
                 rowMeans( permutation[ ,28:38]))/
                (rowSds( permutation [,1:27]) + rowSds( permutation [,28:38]))
                           }

--

David Winsemius
Alameda, CA, USA