[BioC] vector allocation error

Francois Pepin fpepin at aei.ca
Fri Jun 23 20:00:16 CEST 2006

Hi Ulrich,

If you search in the mailing list archive
you'll see a fair number of posts about this problem.

You should look at the just.gcrma function instead. R tends to like
making unnecessary copies of large objects, so people have recoded those
functions (like gcrma) entirely in C which doesn't do that.

I don't know if it'll get you all the way to your 380 arrays. Some
people have suggest doing the normalization in different batches. As I
said the archives should tell you more about it.


On Fri, 2006-06-23 at 14:53 +0200, Ulrich Pfeffer wrote:
> Hi,
> when analyzing more than 25 Affymetrix HGU133plus2 arrays the analysis 
> fails during background correction with GCRMA and the error message says 
> "cannot allocate vector of 301.000kB ...."
> I got the message ot only from my PC but also form a more potent computer 
> (Ml570 G2,  4 CPU XEON MP 2.5/1Mb,
> 16 Gb RAM, s.o.  RH AS 4.0). It does not appear that the computer is using 
> all the memory available.
> After my actual 30 arrays I must analyze 380, which problems will I face?
> Any help?
> Thanx,
> Uli
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