R help - Dec 2010 - my function does not work for large data set

Dear R community,

I have one function, it works for small data set, but does not work on large
data set, can anyone help me with this?
> #creat new variable by dividing each aa dimer by total_length.
> imper<-function(x, file) {
+                    round(x/file$length, 5)
+                     }

> dim(test)
[1]  999 2402
> test[varname[2:2401]]<- apply(as.matrix(test[varname[2:2401]]), 2,
function (x) imper(x, test))

> dim(dimer.nn)
[1] 999554   2402
> dimer.nn[varname[2:2401]]<- apply(as.matrix(dimer.nn[varname[2:2401]]),
2,
function (x) imper(x, dimer.nn))
*
Error in unlist(X, recursive = FALSE, use.names = FALSE) :
  negative length vectors are not allowed*


Thanks so much!

-- 
Sincerely,
Changbin
--

Changbin Du
DOE Joint Genome Institute
Bldg 400 Rm 457
2800 Mitchell Dr
Walnut Creet, CA 94598
Phone: 925-927-2856

	[[alternative HTML version deleted]]

I think that your object exceeds the limit of 2^31 elements. 

Sent from my iPad

On Dec 16, 2010, at 17:44, Changbin Du <changbind at gmail.com> wrote:
> Dear R community,
> 
> I have one function, it works for small data set, but does not work on
large
> data set, can anyone help me with this?
> 
>> #creat new variable by dividing each aa dimer by total_length.
>> imper<-function(x, file) {
> +                    round(x/file$length, 5)
> +                     }
> 
> 
>> dim(test)
> [1]  999 2402
> 
>> test[varname[2:2401]]<- apply(as.matrix(test[varname[2:2401]]), 2,
> function (x) imper(x, test))
> 
> 
>> dim(dimer.nn)
> [1] 999554   2402
> 
>> dimer.nn[varname[2:2401]]<-
apply(as.matrix(dimer.nn[varname[2:2401]]), 2,
> function (x) imper(x, dimer.nn))
> *
> Error in unlist(X, recursive = FALSE, use.names = FALSE) :
>  negative length vectors are not allowed*
> 
> 
> Thanks so much!
> 
> -- 
> Sincerely,
> Changbin
> --
> 
> Changbin Du
> DOE Joint Genome Institute
> Bldg 400 Rm 457
> 2800 Mitchell Dr
> Walnut Creet, CA 94598
> Phone: 925-927-2856
> 
>    [[alternative HTML version deleted]]
> 
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