Re: Help in error removal

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Re: Help in error removal

Mitra, Sumona
Dear all,

I am new to programming in R.
 I deal with microarray data,which is a data frame object type. I need to carry out a few statistical procedures on this, one of them being the pearson corelation. I need to do this between each row which is a gene. So the desired result is a square matrix with the pearson corelation value between each row. So the first column would be (1,1)=0,(1,2),(1,3) and so on.

I uploaded the data frame as "a":-

a <- read.csv("a.csv", header= TRUE, row.names=1)

and then I started the script:-

pearson <- function(a){
 r <- matrix[x,y]
 for(x in as.vector(a[,1], mode="double")){
 x++{
 for(y in as.vector(a[2,], mode="double")){
 y <- x+1
 x++
 {
 r <- (cor.test(as.vector(as.matrix(a)[x,], mode="double"), as.vector(as.matrix(a)[y,], mode="double"))$p.value)
 }
 }
 }
 r[x,y]==r[y,x]
 }
 return(r)
 }

However whenever I run it,I get the error:-

> pearson(a)
Error in matrix[x, y] : object of type 'closure' is not subsettable

Please help!

Best Regards
Sumona Mitra

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Re: Help in error removal

David Winsemius

On Jul 12, 2011, at 7:27 AM, Mitra, Sumona wrote:

> Dear all,
>
> I am new to programming in R.

You see to think there is a "++" operation in R. That is not so.

> I deal with microarray data,which is a data frame object type. I  
> need to carry out a few statistical procedures on this, one of them  
> being the pearson corelation. I need to do this between each row  
> which is a gene. So the desired result is a square matrix with the  
> pearson corelation value between each row. So the first column would  
> be (1,1)=0,(1,2),(1,3) and so on.

I do not understand what that means. You should offer either a minimal  
dataset or at the very least the results of str(a).

>
> I uploaded the data frame as "a":-

If by that you mean you made a failed effort at attaching the data in  
a file, then you need to read the Posting Guide for what the server  
will accept as a file type.

>
> a <- read.csv("a.csv", header= TRUE, row.names=1)
>
> and then I started the script:-
>
> pearson <- function(a){
> r <- matrix[x,y]
> for(x in as.vector(a[,1], mode="double")){

I do not see a need for as.vector here or at any point later.  a[,1]  
would already be a vector and if it is not numeric to begin with, then  
you are going to get junk.

> x++{
> for(y in as.vector(a[2,], mode="double")){
> y <- x+1
> x++
> {
> r <- (cor.test(as.vector(as.matrix(a)[x,], mode="double"),  
> as.vector(as.matrix(a)[y,], mode="double"))$p.value)
> }
> }
> }
> r[x,y]==r[y,x]
> }
> return(r)
> }
>
> However whenever I run it,I get the error:-
>
>> pearson(a)
> Error in matrix[x, y] : object of type 'closure' is not subsettable
>
> Please help!
>
> Best Regards
> Sumona Mitra
>
> ______________________________________________
> [hidden email] 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.

David Winsemius, MD
West Hartford, CT

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Re: Help in error removal

David Hugh-Jones-3
In reply to this post by Mitra, Sumona
On 12 July 2011 12:27, Mitra, Sumona <[hidden email]> wrote:

> Dear all,
>
> I am new to programming in R.
>


You sure are ;-)

 I deal with microarray data,which is a data frame object type. I need to

> carry out a few statistical procedures on this, one of them being the
> pearson corelation. I need to do this between each row which is a gene. So
> the desired result is a square matrix with the pearson corelation value
> between each row. So the first column would be (1,1)=0,(1,2),(1,3) and so
> on.
>
> I uploaded the data frame as "a":-
>
> a <- read.csv("a.csv", header= TRUE, row.names=1)
>
> and then I started the script:-
>
> pearson <- function(a){
>  r <- matrix[x,y]
>

I bet the problem you are getting is here. You want r to be a x by y matrix.
To do this, try r<- matrix(nrow=x, ncol=y). But you haven't defined the x
and y, unless we are missing that part of your code.

As I understand it, you want the correlation matrix between all the rows of
your matrix. If so, then look at the help file for cor. (ie type "?cor".)
You will find that it automatically prints the correlatoins between all
columns of a matrix. So, once your data is correctly read in, you should be
able to just do:

cor(t(a))






>  for(x in as.vector(a[,1], mode="double")){
>  x++{
>  for(y in as.vector(a[2,], mode="double")){
>  y <- x+1
>  x++
>

This code looks like a horrible mess. It's almost never right to loop
through your vectors. In addition, there is no such thing as "++", as
somebody mentioned.



>  {
>  r <- (cor.test(as.vector(as.matrix(a)[x,], mode="double"),
> as.vector(as.matrix(a)[y,], mode="double"))$p.value)
>  }
>  }
>  }
>  r[x,y]==r[y,x]
>  }
>  return(r)
>  }
>
> However whenever I run it,I get the error:-
>
> > pearson(a)
> Error in matrix[x, y] : object of type 'closure' is not subsettable
>
> Please help!
>
> Best Regards
> Sumona Mitra
>
> ______________________________________________
> [hidden email] 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.
>

        [[alternative HTML version deleted]]

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Re: Help in error removal

Mitra, Sumona
In reply to this post by Mitra, Sumona
Dear all,

Thank you so much for your help. I was able to get a script that ran and did what i wanted  it to do. It was as follows:-


> correlation <- function(a)
+ {
+   r <- matrix(nrow = dim(a)[1], ncol=dim(a)[1])
+   for(x in c(2:dim(a)[1]))
+   {
+     for(y in c(x:dim(a)[1]))
+     {
+       r[x,y] <- (cor.test(as.vector(as.matrix(a)[x,], mode="double"), as.vector(as.matrix(a)[y,], mode="double"))$p.value)
+       r[y,x] <- r[x,y]
+     }
+   }
+   return(r)
+ }

Now I want to extend this to include all the possible correlations that cor.test can do. One of the possible arguments of cor.test is method="method", where method can be pearson, spearman or kendall. To include this I modified my code in the following way:-

> correlation <- function(a, b)
+ {
+   r <- matrix(nrow = dim(a)[1], ncol=dim(a)[1])
+   for(x in c(2:dim(a)[1]))
+   {
+     for(y in c(x:dim(a)[1]))
+     {
+       r[x,y] <- (cor.test(as.vector(as.matrix(a)[x,], mode="double"), as.vector(as.matrix(a)[y,], mode="double"), method="b")$p.value)
+       r[y,x] <- r[x,y]
+     }
+   }
+   return(r)
+ }

This when executed though, gives the following error:-

> correlation(a, spearman)
Error in match.arg(method) :
  'arg' should be one of “pearson”, “kendall”, “spearman”

Please help!

Sumona

 
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Re: Help in error removal

David Winsemius

On Jul 13, 2011, at 6:09 AM, Mitra, Sumona wrote:

> Dear all,
>
> Thank you so much for your help. I was able to get a script that ran  
> and did what i wanted  it to do. It was as follows:-
>
>
>> correlation <- function(a)
> + {
> +   r <- matrix(nrow = dim(a)[1], ncol=dim(a)[1])
> +   for(x in c(2:dim(a)[1]))
> +   {
> +     for(y in c(x:dim(a)[1]))
> +     {
> +       r[x,y] <- (cor.test(as.vector(as.matrix(a)[x,],  
> mode="double"), as.vector(as.matrix(a)[y,], mode="double"))$p.value)
> +       r[y,x] <- r[x,y]
> +     }
> +   }
> +   return(r)
> + }
>
> Now I want to extend this to include all the possible correlations  
> that cor.test can do.

You are constructing a technique that in the wrong hands will do very  
bad statistics.

> One of the possible arguments of cor.test is method="method", where  
> method can be pearson, spearman or kendall. To include this I  
> modified my code in the following way:-
>
>> correlation <- function(a, b)
> + {
> +   r <- matrix(nrow = dim(a)[1], ncol=dim(a)[1])
> +   for(x in c(2:dim(a)[1]))
> +   {
> +     for(y in c(x:dim(a)[1]))
> +     {
> +       r[x,y] <- (cor.test(as.vector(as.matrix(a)[x,],  
> mode="double"), as.vector(as.matrix(a)[y,], mode="double"),  
> method="b")$p.value)

If you quote "b", then the interpreter will not substitute the value  
of `b`.

> +       r[y,x] <- r[x,y]
> +     }
> +   }
> +   return(r)
> + }
>
> This when executed though, gives the following error:-
>
>> correlation(a, spearman)
> Error in match.arg(method) :
>  'arg' should be one of “pearson”, “kendall”, “spearman”
>
> Please help!
>
> Sumona

--

David Winsemius, MD
West Hartford, CT

______________________________________________
[hidden email] mailing list
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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.