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 >[[alternative HTML version deleted]]
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 [[alternative HTML version deleted]]
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 >[[alternative HTML version deleted]]