Dear List Members I am confronted with an error when doing hierarchical clustering for expression value clustering in R. > d <- dist(n, method="euclidean") Warning message: In dist(n, method = "euclidean") : NAs introduced by coercion > h <- hclust(d, method="ward") Error in hclust(d, method = "ward") : NA/NaN/Inf in foreign function call (arg 11) It seems that the NAs in my raw data affect it. I tried to remove NAs with the following two ways: d <- na.omit(d) d <- d[rowSums(!is.na(d))!=0, colSums(!is.na(d))!=0] However, they didnot solve the problem. Any comments and suggestions are very appreciated. Thanks! Li

Hi Li, check your data matrix, it looks like it might contain non-numeric data (from the NAs introduced by coercion warning). Try running a 'summary', ploting etc. Best. J. On 15/05/12 23:51, Wang, Li wrote: > Dear List Members > > I am confronted with an error when doing hierarchical clustering for expression value clustering in R. > >> d<- dist(n, method="euclidean") > Warning message: > In dist(n, method = "euclidean") : NAs introduced by coercion >> h<- hclust(d, method="ward") > Error in hclust(d, method = "ward") : > NA/NaN/Inf in foreign function call (arg 11) > > It seems that the NAs in my raw data affect it. > I tried to remove NAs with the following two ways: > d<- na.omit(d) > d<- d[rowSums(!is.na(d))!=0, colSums(!is.na(d))!=0] > > However, they didnot solve the problem. > > Any comments and suggestions are very appreciated. > > Thanks! > Li > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >