[R] Getting error in dendogram based on gene expression

Yogesh Gupta yogesh2cute at gmail.com
Thu Jun 22 10:22:11 CEST 2017

Dear All,

I am trying to make dendogram based on gene expression matrix , but getting
some error:

countMatrix = read.table("count.row.txt",header=T,sep='\t',check.names=F)


count_matrix <- countMatrix[,-1]                   #  remove first column
(gene names)
rownames(count_matrix) <- countMatrix[,1]     #added first column gene
names as rownames)

> nonzero_row <- count_matrix[rowSums(count_matrix) > 0, # removed row sum
0 across all sample

> x1= as.matrix(nonzero_row)                    # converted data into matrix

> x=log2(x1+1)                                          # converted into
log value
> d <- dist(x, method="euclidean")

> h <- hclust(d, method="complete")


 *** caught segfault ***
address 0x7fa39060af28, cause 'memory not mapped'

 1: hclust(d, method = "complete")

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

*Yogesh Gupta*
*Postdoctoral Researcher*
*Department of Biological Science*
*Seoul National University*
*Seoul, South Korea*

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