Hi Ayesha,
I wish to help you, but without a simple self contained example that shows
your issue, I will not be able to help.
Try using the ?dput command to create some simple data, and let us see what
you are doing.
Best,
Tal
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On Fri, May 28, 2010 at 9:04 PM, Ayesha Khan <ayesha.diamond...@gmail.com>wrote:
> 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]]
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