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.atase...@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.ro...@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.atase...@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@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 [[alternative HTML version deleted]] ______________________________________________ R-help@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/posting-guide.html and provide commented, minimal, self-contained, reproducible code.