[R] correlation help

[John Kane]

library(psych)
corr.test(d6)  ?????

--- On Sun, 9/20/09, Adrian Johnson <oriolebaltimore at gmail.com> wrote:

> From: Adrian Johnson <oriolebaltimore at gmail.com>
> Subject: Re: [R] correlation help
> To: r-help at r-project.org
> Received: Sunday, September 20, 2009, 6:19 PM
> thank you john.
> however, I am finding it difficult to automate on a
> matrix.
> 
> Pardon my ignorance in R computing:
> 
> I do not know how to automate on a matrix.
> 
> If I do the following it works:
> > x = cor.test(d6[1,],d6[2,])
> > x
> 
>        Pearson's product-moment
> correlation
> 
> data:  d6[1, ] and d6[2, ]
> t = 10.5196, df = 10, p-value = 9.973e-07
> alternative hypothesis: true correlation is not equal to 0
> 95 percent confidence interval:
>  0.8520623 0.9883592
> sample estimates:
>      cor
> 0.9576655
> 
> 
> If I want to run it on all rows, I do not know how to do
> it.
> 
> I tried following,
> 
> > lapply(d6,cor.test)
> Error in cor.test.default(X[[1L]], ...) :
>  element 1 is empty;
>   the part of the args list of 'length' being
> evaluated was:
>   (y)
> 
> 
> > sapply(d6,cor.test)
> Error in cor.test.default(X[[1L]], ...) :
>  element 1 is empty;
>   the part of the args list of 'length' being
> evaluated was:
>   (y)
> 
> > for(i in 1:14659){
> + k = i+1
> + cor.test(d6[i,],d6[k,])
> + x = cor.test(d6[i,],d6[k,])
> + return(x)}
> Error: no function to return from, jumping to top level
> 
> 
> I appreciate your help.
> 
> thank you.
> Adrian
> 
> On Sun, Sep 20, 2009 at 6:17 PM, Adrian Johnson
> <oriolebaltimore at gmail.com>
> wrote:
> > thank you john.
> > however, I am finding it difficult to automate on a
> matrix.
> >
> > Pardon my ignorance in R computing:
> >
> > I do not know how to automate on a matrix.
> >
> > If I do the following it works:
> >> x = cor.test(d6[1,],d6[2,])
> >> x
> >
> >        Pearson's product-moment correlation
> >
> > data:  d6[1, ] and d6[2, ]
> > t = 10.5196, df = 10, p-value = 9.973e-07
> > alternative hypothesis: true correlation is not equal
> to 0
> > 95 percent confidence interval:
> >  0.8520623 0.9883592
> > sample estimates:
> >      cor
> > 0.9576655
> >
> >
> > If I want to run it on all rows, I do not know how to
> do it.
> >
> > I tried following,
> >
> >> lapply(d6,cor.test)
> > Error in cor.test.default(X[[1L]], ...) :
> >  element 1 is empty;
> >   the part of the args list of 'length' being
> evaluated was:
> >   (y)
> >
> >
> >> sapply(d6,cor.test)
> > Error in cor.test.default(X[[1L]], ...) :
> >  element 1 is empty;
> >   the part of the args list of 'length' being
> evaluated was:
> >   (y)
> >
> >> for(i in 1:14659){
> > + k = i+1
> > + cor.test(d6[i,],d6[k,])
> > + x = cor.test(d6[i,],d6[k,])
> > + return(x)}
> > Error: no function to return from, jumping to top
> level
> >
> >
> > I appreciate your help.
> >
> > thank you.
> > Adrian
> >
> >
> >
> >
> >
> >
> > On Sun, Sep 20, 2009 at 5:13 PM, John Kane <jrkrideau at yahoo.ca>
> wrote:
> >> ?cor
> >> ?cor.test
> >>
> >> --- On Sun, 9/20/09, Adrian Johnson <oriolebaltimore at gmail.com>
> wrote:
> >>
> >>> From: Adrian Johnson <oriolebaltimore at gmail.com>
> >>> Subject: [R] correlation help
> >>> To: r-help at r-project.org
> >>> Received: Sunday, September 20, 2009, 5:00 PM
> >>> Dear group,
> >>>
> >>> I have a matrix like the following:
> >>>
> >>> Name     Sample1
> >>> sample2    sample3   sample4 .....
> >>> sample(n)
> >>> nm1        10.5
> >>>     13.5
> >>> 30             31
> >>> nm2         8
> >>>           11
> >>>       34
> >>>    29
> >>> nm3         9
> >>>           10.3
> >>>     27.8         35
> >>> nm(j)
> >>>
> >>>
> >>> I want to be able to calculate correlation
> between
> >>> all pairs of names.
> >>> For example (nm1,nm2), (nm1,nm3), (nm1,nmj),
> (nm2,nm3),
> >>> (nm2,nmj)....
> >>>
> >>> Then I want to calculate the significance of
> correlation
> >>> using t-score
> >>> or p-value.
> >>>
> >>> I can calculate correlation coeffecient in
> excel but not
> >>> significance
> >>> in both excel and R.
> >>>
> >>> I want to be able to do it in R, I appreciate
> your help.
> >>> thank you.
> >>> Ad.
> >>>
> >>>
> ______________________________________________
> >>> R-help at r-project.org
> >>> mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-help
> >>> 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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________________________
> R-help at r-project.org
> mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> 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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