I can't run your code.
Please, just give me whatever comes on your screen when you run:
dput(q)
On Fri, May 28, 2010 at 10:57 PM, Ayesha Khan
<ayesha.diamond...@gmail.com>wrote:
> I assume my matrix should look something like this?..
>
> >round(distance, 4)
> P00A P00B M02A M02B P04A P04B M06A M06B P08A P08B
> M10A
> P00B 0.9678
> M02A 1.0054 1.0349
> M02B 1.0258 1.0052 1.2106
> P04A 1.0247 0.9928 1.0145 0.9260
> P04B 0.9898 0.9769 0.9875 0.9855 0.6075
> M06A 1.0159 0.9893 1.0175 0.9521 0.9266 0.9660
> M06B 0.9837 0.9912 1.0124 1.0402 1.0272 1.0367 1.5693
> P08A 1.0279 1.0303 0.9865 0.9748 1.0184 1.0452 0.9799 1.0400
> P08B 1.0248 1.0299 0.9717 0.9673 1.0048 1.0329 1.0280 0.9907 0.2158
> M10A 0.9850 0.9603 1.0246 0.9708 1.0231 0.9771 0.9916 1.0168 0.9722 0.9525
> M10B 1.0150 1.0397 0.9754 1.0292 0.9769 1.0229 1.0084 0.9832 1.0278 1.0475
> 2.0000
>
>
>
> On Fri, May 28, 2010 at 3:39 PM, Ayesha Khan
> <ayesha.diamond...@gmail.com>wrote:
>
>> v <- dput(x,"sampledata.txt")
>> dim(v)
>> q <- v[1:10,1:10]
>> f =as.matrix(dist(t(q)))
>>
>> distB=NULL
>> for(k in 1:(nrow(f)-1)) for( m in (k+1):ncol(f)) {
>> if(f[k,m] <2) distB=rbind(distB,c(k,m,f[k,m]))
>> }
>> #now distB looks like this
>>
>> > distB
>> [,1] [,2] [,3]
>> [1,] 1 2 1.6275568
>> [2,] 1 3 0.5252058
>> [3,] 1 4 0.7323116
>> [4,] 1 5 1 .9966001
>> [5,] 1 6 1.6664110
>> [6,] 1 7 1.0800540
>> [7,] 1 8 1.8698925
>> [8,] 1 10 0.5161808
>> [9,] 2 3 1.7325811
>> [10,] 2 5 0.8267843
>> [11,] 2 6 0.5963280
>> [12,] 2 7 0.8787230
>>
>> #now from this output< i want to cluster all 1's, friedns of 1 and friends
>> of friends of 1 in one cluster. The same goes for 2,3 and so on
>> But when i do that using hclust, i get the following error. I think what I
>> need to do is convert my cureent matrix somehow into a format that would be
>> accepted by the hclust function but I dont know how to achieve that.
>> distclust <- hclust(distB,method="single")
>>
>> Error in if (n < 2) stop("must have n >= 2 objects to cluster") :
>> argument is of length zero
>>
>> P.S: Please let me know if this makes things more clear? "cuz i dont know
>> how looking at the original data set would help becuase the matrix under
>> consdieration right now is the distance matrix and how it can be altered. I
>> have tried as.dist, doesnt work because my matrix as i mentioned eralier is
>> not a square matrix.
>>
>> On Fri, May 28, 2010 at 2:37 PM, Tal Galili <tal.gal...@gmail.com>wrote:
>>
>>> 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
>>> ----------------Contact
>>> Details:-------------------------------------------------------
>>> Contact me: tal.gal...@gmail.com | 972-52-7275845
>>> Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
>>> www.r-statistics.com (English)
>>>
>>> ----------------------------------------------------------------------------------------------
>>>
>>>
>>>
>>>
>>> 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
>>>>
>>>
>>>
>>
>>
>> --
>> Ayesha Khan
>>
>> MS Bioengineering
>> Dept. of Bioengineering
>> Rice University, TX
>>
>
>
>
> --
> Ayesha Khan
>
> MS Bioengineering
> Dept. of Bioengineering
> Rice University, TX
>
--
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
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