R help - Aug 2014 - How to do t.test to rows of a dataframe using apply family function?

Hi All?
How to do t.test  to rows (with two levels, or in other words, groups of
samples) of a dataframe using apply family function? I have done that using
function and loops. And my overall purpose is to calculate DE genes from two
groups of miRNA microarray samples. And I know limma can do that, but it seems
limma doesn't support paired t-test.

t.test.df=function(df,paired){
  df.t=c()
  for(i in 1:nrow(df)){
    df.t=rbind(df.t,unlist(t.test(df[i,grp1],df[i,grp2],paired=paired)))
  }
  rownames(df.t)=rownames(df)
  df.t
}

Bests!
Allen Chiu

2014-08-26
	[[alternative HTML version deleted]]

Hi

If your function works for you why to bother with apply? If it does not give you
required results, please post some data and show us what is expected.

I would remove unlist from your function and declare list for storing data,
which seems to me more natural for storing results.

t.test.list=function(df,paired){
   lll<-vector("list", length=nrow(df))
   for(i in 1:nrow(df)){

 lll[[i]]=t.test(df[i,grp1],df[i,grp2],paired=paired)
   }
  names(lll)=rownames(df)
   lll
> }
Regards
Petr

> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> project.org] On Behalf Of my1stbox
> Sent: Tuesday, August 26, 2014 3:26 AM
> To: R Help
> Subject: [R] How to do t.test to rows of a dataframe using apply family
> function?
>
> Hi All?
> How to do t.test  to rows (with two levels, or in other words, groups
> of samples) of a dataframe using apply family function? I have done
> that using function and loops. And my overall purpose is to calculate
> DE genes from two groups of miRNA microarray samples. And I know limma
> can do that, but it seems limma doesn't support paired t-test.
>
> t.test.df=function(df,paired){
>   df.t=c()
>   for(i in 1:nrow(df)){
>
> df.t=rbind(df.t,unlist(t.test(df[i,grp1],df[i,grp2],paired=paired)))
>   }
>   rownames(df.t)=rownames(df)
>   df.t
> }
>
> Bests!
> Allen Chiu
>
> 2014-08-26
>       [[alternative HTML version deleted]]
>
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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.
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