Question: read.delim taking infinite time in edgeR analysis
0
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.

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
[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

modified 20 months ago • written 20 months ago by fawazfebin30
2
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.

0
20 months ago by
fawazfebin30
fawazfebin30 wrote:
Great thanks Aaron ! Shall check on it.