[R] PAM Clustering

[Sema Atasever]

Grazie mille,

So grateful for your kindness in answering questions.

Regards.



On Thu, Aug 17, 2017 at 8:50 PM, Germano Rossi <germano.rossi at gmail.com>
wrote:

> Sorry, I never use pam. In the help, you can see that pam require a
> dataframe OR a dissimilarity matrix. If diss=FALSE then "euclidean" was
> use.So, I interpret that a matrix of dissimilarity is generated
> automatically.
>
> Problems may be in your data. Indeed
>
> pam(ruspini, 4)$diss
>
> write a dissimilaty matrix
>
> while
> pam(MYdata,10)$diss
>
> wite NULL
>
>
> 2017-08-17 16:03 GMT+02:00 Sema Atasever <s.atasever at gmail.com>:
>
>> Dear Germano,
>>
>> Thank you for your fast reply,
>>
>> In the above code, *MYData *is the actual data set.
>>
>> Do not we need to convert *MYData to *the dissimilarity matrix using
>> *pam(as.dist(**MYData**), k = 10, diss = TRUE*)*   code line?*
>>
>> *Regards.*
>>
>> On Thu, Aug 17, 2017 at 2:58 PM, Germano Rossi <germano.rossi at gmail.com>
>> wrote:
>>
>>> try this
>>>
>>> MYdata <- read.csv2("data.txt",dec='.')
>>> library(cluster)
>>> cluster.pam = pam(MYdata,10)
>>> table(cluster.pam$clustering)
>>> filenameclu = paste("clusters", ".txt")
>>> write.table(cluster.pam$clustering, file=filenameclu,sep=",")
>>>
>>>
>>> 2017-08-17 10:28 GMT+02:00 Sema Atasever <s.atasever at gmail.com>:
>>>
>>>> Dear Authorized Sir / Madam,
>>>>
>>>> I have a data set in which each row indicates an amino asid and each
>>>> column corresponds
>>>> to a feature (in total 539 features).
>>>> I want to use PAM Clustering usign this data set.
>>>>
>>>>
>>>> *when i ran R script i am getting this error:*
>>>> *Error in pam(d, 10) : x is not a numeric dataframe or matrix.*
>>>> *Execution halted*
>>>>
>>>> How can i fix this error? Is there a problem with my dataset?
>>>>
>>>> Thanks in advance.
>>>>
>>>>
>>>> *PAM clustering codes:*
>>>>
>>>> MYdata <- read.csv2("data.txt", dec = ".")
>>>> attach(MYdata)
>>>> d=as.matrix(MYdata)
>>>> library(cluster)
>>>> cluster.pam = pam(d,10)
>>>> table(cluster.pam$clustering)
>>>>
>>>> filenameclu = paste("clusters", ".txt")
>>>> write.table(cluster.pam$clustering, file=filenameclu,sep=",")
>>>>
>>>> ______________________________________________
>>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>> PLEASE do read the posting guide http://www.R-project.org/posti
>>>> ng-guide.html
>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>
>>>
>>>
>>>
>>> --
>>> ==================
>>> Germano Rossi, Dipartimento di Psicologia, Universita' degli Studi di
>>> Milano Bicocca
>>> Piazza dell'Ateneo Nuovo, 1- 20126 Milano - Italy
>>>
>>
>>
>
>
> --
> ==================
> Germano Rossi, Dipartimento di Psicologia, Universita' degli Studi di
> Milano Bicocca
> Piazza dell'Ateneo Nuovo, 1- 20126 Milano - Italy
>

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