How to read large GEO series matrix file when getGEO fails

Question

[hzc363]

I tried to read the GEO series matrix file (GSE37138) into R using the getGEO function from the GEOquery package. The matrix file is quite large (2.8GB after un-zip). My R session always crashes when trying to read the file.

I have read a 4GB csv file into R using the fread function from data.table package before. So my computer should be able to handle the 2.8GB GEO series matrix file. Are there any other efficient ways to read the series matrix file into R?

[Kevin Blighe]

What's the exact error message that R returns?; Are you trying to read the data into a session that's already full of other variables?

[hzc363]

There is no error message, the R stopped responding. The same thing happened even after I restarted my computer.

[Kevin Blighe]

Okay, why not download it manually from here: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE37nnn/GSE37138/matrix/