did not converge in 10 iterations

fviz_nbclust (kmeans) with method “gap_stat” error: did not converge in 10 iterations


Dear all,

im trying to find the optimum number of clusters to fit to a gene expression dataset.

For this, Im using the packages FactoMineR and factoextra and the function fviz_nbclust on my scaled dataframe (simple dataframe with genes in rows and samples in columns).

It scales (z-scoring) by column so im transposing first and then scaling. Then i retranspose and calculate the optimal number of clusters.

The problem is that i get a Warning message ” did not converge in 10 iterations “.
The question is, do you know a way to modify the number of iteractions?

This is the code im using

df <- scale (t(mydata))
df <- t(df)
fviz_nbclust(df, kmeans, method = "gap_stat")
fit <- kmeans(df, ?) 
mydata2 <- data.frame(df, fit$cluster)

?: this value is dictated by the clusters prediction

Thanks in advance




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