[R] memory limit in aov

[Lucy Crooks]

I want to do an unbalanced anova on 272,992 observations with 405  
factors including 2-way interactions between 1 of these factors and  
the other 404. After fitting only 11 factors and their interactions I  
get error messages like:

Error: cannot allocate vector of size 1433066 Kb
R(365,0xa000ed68) malloc: *** vm_allocate(size=1467461632) failed  
(error code=3)
R(365,0xa000ed68) malloc: *** error: can't allocate region
R(365,0xa000ed68) malloc: *** set a breakpoint in szone_error to debug

I think that the anova involves a matrix of 272,992 rows by 29025  
columns (using dummy variables)=7,900 million elements. I realise  
this is a lot! Could I solve this if I had more RAM or is it just too  
big?

Another possibility is to do 16 separate analyses on 17,062  
observations with 404 factors (although statistically I think the  
first approach is preferable). I get similar error messages then:

Error: cannot allocate vector of size 175685 Kb
R(365,0xa000ed68) malloc: *** vm_allocate(size=179904512) failed  
(error code=3)

I think this analysis requires a 31 million element matrix.

I am using R version 2.2.1 on a Mac G5 with 1 GB RAM running OS  
10.4.4. Can somebody tell me what the limitations of my machine (or  
R) are likely to be? Whether this smaller analysis is feasible? and  
if so how much more memory I might require?

The data is in R in a data frame of 272,992 rows by 406 columns. I  
would really appreciate any helpful input.

Lucy Crooks
Theoretical Biology
ETH Zurich