[BioC] memory requirement
Liaw, Andy
andy_liaw@merck.com
Tue, 26 Nov 2002 08:26:02 -0500
Depends on how much memory you want R to be able to use. If you want R to
use more than 1GB (and you have more than 1GB), then yes, you should add the
--max-mem-size argument.
This is an "improvement" only in the sense that you're giving R more to play
with.
Andy
-----Original Message-----
From: Tom McCarty [mailto:TMCCARTY@niaid.nih.gov]
Sent: Tuesday, November 26, 2002 8:13 AM
To: 'Liaw, Andy'; 'Stephen Henderson'
Cc: 'bioconductor@stat.math.ethz.ch'
Subject: RE: [BioC] memory requirement
So if I have more than 1 GB of RAM, following the previous suggestion is the
best way to improve memory allocation to R?
Tom McCarty
-----Original Message-----
From: Liaw, Andy [ mailto:andy_liaw@merck.com <mailto:andy_liaw@merck.com> ]
Sent: Tuesday, November 26, 2002 8:01 AM
To: 'Stephen Henderson'
Cc: 'bioconductor@stat.math.ethz.ch'
Subject: RE: [BioC] memory requirement
If you've upgraded to R-1.6.1, note that the limit on Windows has been
raised to the smaller of physical RAM and 1GB (used to be 256MB). So unless
you have more than 1GB of RAM, there's no need to do that.
Andy
-----Original Message-----
From: Stephen Henderson [ mailto:s.henderson@ucl.ac.uk
<mailto:s.henderson@ucl.ac.uk> ]
Sent: Tuesday, November 26, 2002 6:52 AM
To: 'Laurent Gautier'
Cc: 'bioconductor@stat.math.ethz.ch'
Subject: RE: [BioC] memory requirement
Here is the advice given to me on improving R memory on Win some time ago on
this very list from --Tibor van. This helped a bit.
If you have a shortcut on your desktop for R (or somewhere else), then if
you right click on the icon and bring up the Properties window, you will see
an entry for
Target with the path to the executable filled in. After that path (and
outside of the quotes) add this command-line argument on my PC, for example
it would look like this:
"C:\Program Files\R\rw1051\bin\Rgui.exe" --max-mem-size=768M
Restart R and you will be in business...
Stephen Henderson
Wolfson Institute for Biomedical Research
UCL, London
-----Original Message-----
From: Laurent Gautier [ mailto:laurent@cbs.dtu.dk
<mailto:laurent@cbs.dtu.dk> ]
Sent: Tuesday, November 26, 2002 12:57 AM
To: Wilkinson, Mark
Cc: 'bioconductor@stat.math.ethz.ch'
Subject: Re: [BioC] memory requirement
On Mon, Nov 25, 2002 at 03:43:08PM -0600, Wilkinson, Mark wrote:
> Here, here. I'd've asked sooner, but suspected I'd be advised the brute
> force approach of beefing up my machine.
>
> I'm running the affy package, specifically, with U133 chips, but am only
> able to read in 10-15 CEL files at once. Any way around this? I've
> considered using 'merge' to read a few, merge, read a few more, merge,
etc.
> I'm using Windows R, which seems to have poor memory management anyway.
Any
> tips?
>
How much memory did you have ?
I do not know much of the behavior with Windows, but with linux I remember
doing
the full monty (raw data -> normalization -> summary expression value) for
about 80 U95A at once on a machine with 2Gb.
note : the new release of the package spits out something with the size of
the 'AffyBatch' object with the default print method (try:
data(Dilution)
Dilution
)
Hopin' it helps,
L.
>
> Mark Wilkinson
> Informatics Analyst
> St. Jude Children's Research Hospital
> Department of Pharmaceutical Sciences
>
>
> -----Original Message-----
> From: Yi-Xiong Zhou [ mailto:yzhou@arcturusag.com
<mailto:yzhou@arcturusag.com> ]
> Sent: Monday, November 25, 2002 3:24 PM
> To: 'bioconductor@stat.math.ethz.ch'
> Subject: [BioC] memory requirement
>
> I am concerning the memory requirement of running bioconductor on Affy
> chips. Could you give me an estimate?
>
> Thanks.
>
> Yi-Xiong
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
<http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
<http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor>
--
--------------------------------------------------------------
Laurent Gautier CBS, Building 208, DTU
PhD. Student DK-2800 Lyngby,Denmark
tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent
<http://www.cbs.dtu.dk/laurent>
_______________________________________________
Bioconductor mailing list
Bioconductor@stat.math.ethz.ch
http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
<http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor>
**********************************************************************
This email and any files transmitted with it are confidential and
intended solely for the use of the individual or entity to whom they
are addressed. If you have received this email in error please notify
the system manager (wibr.mail@ucl.ac.uk). All files are scanned for viruses.
**********************************************************************
[[alternate HTML version deleted]]
_______________________________________________
Bioconductor mailing list
Bioconductor@stat.math.ethz.ch
http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
<http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor>
----------------------------------------------------------------------------
--
Notice: This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (Whitehouse Station, New Jersey, USA) that
may be confidential, proprietary copyrighted and/or legally privileged, and
is intended solely for the use of the individual or entity named in this
message. If you are not the intended recipient, and have received this
message in error, please immediately return this by e-mail and then delete
it.
============================================================================
==
_______________________________________________
Bioconductor mailing list
Bioconductor@stat.math.ethz.ch
http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
<http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor>
------------------------------------------------------------------------------
Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (Whitehouse Station, New Jersey, USA) that may be confidential, proprietary copyrighted and/or legally privileged, and is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please immediately return this by e-mail and then delete it.
==============================================================================
[[alternate HTML version deleted]]