[BioC] problem with vsn and affy data...

[Oliver Hartmann]

Dear list members,

I am running into the error message

Error: cannot allocate vector of size 22776 Kb.

This is on a WinNT computer with 1 GB RAM, 1.8 GB RAM allocated to R 
(~1GB was in use bevor the error occured). I analyzed 24 affy Hg_u95a 
chips with R 1.6.1, Bioconductor 1.1, affy 1.1.1.
I have analyzed 34 Affy chips (rma method) with Bioconductor 1.0 bevor 
(using a total of ~1.5 GB RAM) as well as 8 Affy Hg_u95a chips with R 
1.6.1, Bioconductor 1.1, affy 1.1.1. (vsn and rma).

The R script I used was

 > normalize.AffyBatch.methods <- c(normalize.AffyBatch.methods, "vsn")
 > f <- express(data, bg="subtractmm", normalize.method="vsn", 
summary.stat=avdiff)

and I got:

Normalizing Data
Called vsn on 201807x24 matrix, with lts.quantile=0.75 and niter=10. 
This may take a while.

This broke off after iter 7. Any ideas?

Thanks a lot

	-oliver hartmann-
-- 
Oliver Hartmann, Institute of Medical Biometry and Epidemiology
Philipps-University Marburg, Bunsenstr. 3, D-35037 Marburg
phone +49(0)6421 28 66514, fax +49(0)6421 28 68921