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

[Stephen Henderson]

Sorry.

What is the vsn method you're talking about? I don't see this in my
normalize.AffyBatch.methods

Stephen Henderson

-----Original Message-----
From: Wolfgang Huber [mailto:w.huber@dkfz-heidelberg.de] 
Sent: Wednesday, December 18, 2002 3:11 PM
To: Oliver Hartmann; bioconductor
Subject: RE: [BioC] problem with vsn and affy data...

Hi Oliver,

the 201807 x 24 data matrix uses ca. 38 MB of memory (assuming 8 byte per
double). Even if this data is copied back and forth a couple of times the
total memory usage should not overrun 1 GB. So it seems to me more like a
bug -either in vsn or in R- than just the "normal" excessive memory
consumption.

Have you tried with gc() before calling express() ?

Otherwise, if you email me the necessary script and data set or put it on a
ftp/http server I could offer you to try to reproduce the error here, both
on windows or on a bigger Unix machine, and see what's causing it.

Also, you can try different values for the parameters of vsn than the
default (niter=10, lts.quantile=0.75). niter=5 and lts.quantile=0.5 should
be sufficient for affy data and save some computing time.  There was a
problem with the affy::expresso/vsn interface shortly before the release in
November, so can you please make sure you use the most recent version 1.0.1.
of vsn?

Best regards

Wolfgang Huber

Division of Molecular Genome Analysis (Dep. Poustka)
German Cancer Research Center (DKFZ)
Im Neuenheimer Feld 580
69120 Heidelberg, Germany

w.huber@dkfz.de
http://www.dkfz.de/abt0840/whuber
Tel +49-6221-424709
Fax +49-6221-42524709


-----Original Message-----
From: bioconductor-admin@stat.math.ethz.ch
[mailto:bioconductor-admin@stat.math.ethz.ch]On Behalf Of Oliver
Hartmann
Sent: Wednesday, December 18, 2002 9:01 AM
To: bioconductor@stat.math.ethz.ch
Subject: [BioC] problem with vsn and affy data...


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

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