Question: 450k methylation data: error loading
0
gravatar for nickswim9
4.8 years ago by
nickswim90
nickswim90 wrote:

I'm having trouble loading the series matrix data into R.  I downloaded the file from this link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60132

I then saved it on my desktop.  Below is the code and error message I'm getting.

 

> setwd("C:/Users/Nick/Desktop")
> data <- read.delim(file = "GSE60132_series_matrix.txt")
Error: cannot allocate vector of size 349.1 Mb
In addition: Warning messages:
1: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
  Reached total allocation of 8048Mb: see help(memory.size)
2: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
  Reached total allocation of 8048Mb: see help(memory.size)
3: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
  Reached total allocation of 8048Mb: see help(memory.size)
4: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
  Reached total allocation of 8048Mb: see help(memory.size)
> data <- read.delim(file = "GSE60132_series_matrix.txt", row.names=1)
methylation geo illumina 450k • 1.5k views
ADD COMMENTlink modified 4.8 years ago by Devon Ryan96k • written 4.8 years ago by nickswim90
1
gravatar for Devon Ryan
4.8 years ago by
Devon Ryan96k
Freiburg, Germany
Devon Ryan96k wrote:

You're running out of memory, you might want to try a different computer (or possibly reboot and do this first with nothing else running...perhaps you'll have enough free then).

ADD COMMENTlink written 4.8 years ago by Devon Ryan96k
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