[R] PAM Clustering

[Sema Atasever]

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=",")
>>
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>>
>
>
>
> --
> ==================
> Germano Rossi, Dipartimento di Psicologia, Universita' degli Studi di
> Milano Bicocca
> Piazza dell'Ateneo Nuovo, 1- 20126 Milano - Italy
>

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