Problem: You see some variant of the error
Though the number 330MB seems small enough for todays computers, R only reports the last failed allocation.
- Try Linux (or 64bit windows) !
- Possible to try R 3.0.0 (current devel as of Jan 2013, stable release scheduled for May)
Please check the R-on-windows-FAQ. There are some hints to get a little bit more memory available to R on windows. Generally, R runs faster and smoother on Linux.
You might try to export the files in centroid mode to reduce memory consumption or use R under linux instead of windows. More ideas are in ReduceFileSizes (http://http://metabolomics-forum.com/viewtopic.php?f=25&t=147&sid=f013b96068389bb2cd72ebf21c448690).