I am concerning the memory requirement of running bioconductor on Affy chips. Could you give me an estimate? Thanks. Yi-Xiong

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? Mark Wilkinson Informatics Analyst St. Jude Children's Research Hospital Department of Pharmaceutical Sciences -----Original Message----- From: Yi-Xiong Zhou [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

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] 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] 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] > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > 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 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch 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 ---------------------------------------------------------------------- -------- 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. ====================================================================== ========

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] 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] 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] 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] > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > 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 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch 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 ---------------------------------------------------------------------- ------ -- 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 [[alternate HTML version deleted]]

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]]

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] 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] > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > 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 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch 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]]