Message-ID: <CAAjHrnMX18U9Lam+gj+eb=OTN1YWhB5+yTxTKV04CDAG1aoR9g@mail.gmail.com>
Date: 2017-06-22T08:22:11Z
From: Yogesh Gupta
Subject: Getting error in dendogram based on gene expression
Dear All,
I am trying to make dendogram based on gene expression matrix , but getting
some error:
I
countMatrix = read.table("count.row.txt",header=T,sep='\t',check.names=F)
colnames(countMatrix)
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")
*Error:*
*** caught segfault ***
address 0x7fa39060af28, cause 'memory not mapped'
Traceback:
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
Selection:
Thanks
Yogesh
--
*Yogesh Gupta*
*Postdoctoral Researcher*
*Department of Biological Science*
*Seoul National University*
*Seoul, South Korea*
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