Thanks Tal & Joris!
I created my distance matrix distA by using the dist() function in R
manipulating my output in order to get a matrix.
distA =as.matrix(dist(t(x2))) # x2 being my original dataset
as according to the documentaion on dist()
For the default method, a "dist" object, or a matrix (of distances) or an
object which can be coerced to such a matrix using as.matrix()
On Fri, May 28, 2010 at 6:34 AM, Joris Meys <jorism...@gmail.com> wrote:
> As Tal said.
>
> Next to that, I read that column1 (and column2?) are supposed to be seen as
> factors, not as numerical variables. Did you take that into account somehow?
>
> It's easy to reproduce the error code :
> > n <- NULL
> > if(n<2)print("This is OK")
> Error in if (n < 2) print("This is OK") : argument is of length zero
>
> In the hclust code, you find following line :
> n <- as.integer(attr(d, "Size"))
> where d is the distance object entered in the hclust function. Looking at
> the error you get, this means that the size attribute of your distance is
> NULL. Which tells me that distA is not a dist-object.
>
> > A <- matrix(1:4,ncol=2)
> > A
> [,1] [,2]
> [1,] 1 3
> [2,] 2 4
> > hclust(A,method="single")
>
> Error in if (n < 2) stop("must have n >= 2 objects to cluster") :
> argument is of length zero
>
> Did you actually put in a distance object? see also ?dist or ?as.dist.
>
> Cheers
> Joris
>
>
>
>
> On Fri, May 28, 2010 at 1:41 AM, Ayesha Khan <ayesha.diamond...@gmail.com
> > wrote:
>
>> i have a matrix with the following dimensions
>> 136 3
>>
>> and it looks something like
>>
>> [,1] [,2] [,3]
>> [1,] 402 675 1.802758
>> [2,] 402 696 1.938902
>> [3,] 402 699 1.994253
>> [4,] 402 945 1.898619
>> [5,] 424 470 1.812857
>> [6,] 424 905 1.816345
>> [7,] 470 905 1.871252
>> [8,] 504 780 1.958191
>> [9,] 504 848 1.997111...............
>>
>> ................................................................................
>> so you get the idea. I want to group similar items in one group/cluster
>> following the "friends of friends" approach. I tried doing
>>
>> distclust <- hclust(distA,method="single")
>> However, I got the following error.
>>
>> Error in if (n < 2) stop("must have n >= 2 objects to cluster") :
>> argument
>> is of length zero
>> which probably means there's something wrong with my input here. Is there
>> another way of doing this kind of clustering without getting into all the
>> looping and ifelse etc. Basically, if 402 is close to 675,696,and699 and
>> thus fall in cluster A then all items close to 675,696,and 699 should also
>> fall into the same cluster A following a friends of friedns strategy.
>> Any help would be highly appreciated.
>>
>> --
>> Ayesha Khan
>>
>> MS Bioengineering
>> Dept. of Bioengineering
>> Rice University, TX
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help@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<http://www.r-project.org/posting-guide.html>
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
>
> --
> Joris Meys
> Statistical Consultant
>
> Ghent University
> Faculty of Bioscience Engineering
> Department of Applied mathematics, biometrics and process control
>
> Coupure Links 653
> B-9000 Gent
>
> tel : +32 9 264 59 87
> joris.m...@ugent.be
> -------------------------------
> Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
>
--
Ayesha Khan
MS Bioengineering
Dept. of Bioengineering
Rice University, TX
[[alternative HTML version deleted]]
______________________________________________
R-help@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.
