Question: read.delim taking infinite time in edgeR analysis
0
gravatar for fawazfebin
20 months ago by
fawazfebin30
fawazfebin30 wrote:

Hi

I was using the read.delim function on a gene counts file to construct a table of gene counts for six samples for performing edgeR differential expression analysis. The input counts file (27.4 MB file) is in the ~/ directory. But the command seems running for an infinite time with no return of R prompt or any errors. Is there any reason behind such a run ? I have been trying it for a plenty of times and the same issue arises again. I even tried to reinstall R and R-studio. The command and sessionInfo () are given below.

> read.delim ("~/DEXcounts.txt", row.names = NULL, header =TRUE )

Here is my sessionInfo() :

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_IN.UTF-8       LC_NUMERIC=C               LC_TIME=en_IN.UTF-8       
 [4] LC_COLLATE=en_IN.UTF-8     LC_MONETARY=en_IN.UTF-8    LC_MESSAGES=en_IN.UTF-8   
 [7] LC_PAPER=en_IN.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.4.3 tools_3.4.3  

 

Can anyone help please. Thanks in advance.

 

 

edger read.delim • 342 views
ADD COMMENTlink modified 20 months ago • written 20 months ago by fawazfebin30
Answer: read.delim taking infinite time in edgeR analysis
2
gravatar for Aaron Lun
20 months ago by
Aaron Lun25k
Cambridge, United Kingdom
Aaron Lun25k wrote:

read.delim is a function from the utils package, rather than edgeR, so this is not really an edgeR problem. You'd be better off asking this question in a more general R programming forum, e.g., StackOverflow.

I am not aware of any circumstances that cause read.delim to hang; I would suggest checking that the file is actually (i) tab-separated, (ii) contains only numeric values in the matrix and (iii) properly new-lined. If it is just a case of the file being very large relative to your computer's abilities, you might consider using other, faster methods of data import, e.g., fread from data.table.

ADD COMMENTlink modified 20 months ago • written 20 months ago by Aaron Lun25k
Answer: read.delim taking infinite time in edgeR analysis
0
gravatar for fawazfebin
20 months ago by
fawazfebin30
fawazfebin30 wrote:
Great thanks Aaron ! Shall check on it.
ADD COMMENTlink written 20 months ago by fawazfebin30
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