Dear BC-list,

 

I've recently started analyzing several Human Affymetrix HGU133 Plus 2.0
arrays using R 2.2.1 for Win32. This was done for 2 experiments: (A)
containing 16 chips, while (B) was performed on 24 chips. Using the
'qc'- and the 'gcrma'-function did not result in any problems for the
(A)-batch, but the (B)-batch showed the following:

 

> quality<-qc(rawdata_B)

Background correcting

Error: cannot allocate vector of size 254043Kb

> 

 

My first guess would have been that there was not enough memory
allocated in R itself, hence I increased the global memory limit to
approximately 4 Gb (memory.limit(size=4000)). Redoing the same steps
resulted in an identical error. The pc used for this purpose contains 2
GB of physical RAM.

 

Is there a specific memory module/function allocated to vector sizes,
and if so, how is it called (and moreover, how can this be increased)?
Or is something else happening here?

 

Kind regards,

 

   Stan


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