>>>>> Yogesh Gupta <yogesh2c...@gmail.com>
>>>>> on Wed, 21 Jun 2017 13:42:15 +0900 writes:
> 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:
This looks like a problem that should not happen.
Though it could be that it's just too large a problem (for your
hardware, or "in general").
However, we cannot reproduce what you show above.
To help us help you please provide (to this mailing list!)
- a (minimal) reproducible example
- sessionInfo()
It is best to take time to carefully read
https://www.r-proejct.org/help.html
and/or then just search "reproducible example R" :
http://lmgtfy.com/?q=reproducible+example+R
Martin
> Thanks
> Yogesh
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