Yogesh Gupta
2017-Jun-21 04:42 UTC
[R] getting error while trying to make dendogram based on gene expression
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
[[alternative HTML version deleted]]
Martin Maechler
2017-Jun-23 09:23 UTC
[R] getting error while trying to make dendogram based on gene expression
>>>>> Yogesh Gupta <yogesh2cute at 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