R memory limit
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@hernando-martinez-4124
Last seen 10.2 years ago
Hi, I am working with large data, and when I try to read it into R using 'ReadAffy', I get the following error message: "cannot allocate a vector size 712Mb". I have a MacBook Pro with 4Gb of memory. I have been reading some posts online, but I haven't found a clear solution. Maybe is a limit in R, or an imposed limit of my system that I should change. Does anyone knows how to do it? Any ideas? Many thanks, -- Hernando Martínez Vergara [[alternative HTML version deleted]]
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@benilton-carvalho-1375
Last seen 4.7 years ago
Brazil/Campinas/UNICAMP
You didn't provide us the information described in the post guide (sessionInfo and description of the issue). R does not impose any limit. What is the type of array you're trying to analyze? And what preprocessing strategy would you like to apply? How many samples do you have? Are you using R in 32 or 64 bit mode? You may be interested in taking a look at justRMA(), if RMA is your choice. If you're in 32 bit mode, you definitely want to load R in 64 bit... With more detailed information, we're going to be able to help you out. b On 14 June 2010 14:36, Hernando Mart?nez <hernybiotec at="" gmail.com=""> wrote: > Hi, I am working with large data, and when I try to read it into R using > 'ReadAffy', I get the following error message: "cannot allocate a vector > size 712Mb". I have a MacBook Pro with 4Gb of memory. I have been reading > some posts online, but I haven't found a clear solution. Maybe is a limit in > R, or an imposed limit of my system that I should change. Does anyone knows > how to do it? Any ideas? > > Many thanks, > > -- > Hernando Mart?nez Vergara > > ? ? ? ?[[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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sorry, I am trying to analize an expression microarray of nearly 350 samples. My R version is R 2.10.1 GUI 1.31 Leopard build 32-bit (5537). How do I load R in 64 bit? (maybe this is a trivial question for you but it is not for me, as I have no computer background). Thank you very much again, Hernando 2010/6/14 Benilton Carvalho <beniltoncarvalho@gmail.com> > You didn't provide us the information described in the post guide > (sessionInfo and description of the issue). > > R does not impose any limit. > > What is the type of array you're trying to analyze? And what > preprocessing strategy would you like to apply? How many samples do > you have? Are you using R in 32 or 64 bit mode? > > You may be interested in taking a look at justRMA(), if RMA is your > choice. If you're in 32 bit mode, you definitely want to load R in 64 > bit... > > With more detailed information, we're going to be able to help you out. > > b > > On 14 June 2010 14:36, Hernando Martínez <hernybiotec@gmail.com> wrote: > > Hi, I am working with large data, and when I try to read it into R using > > 'ReadAffy', I get the following error message: "cannot allocate a vector > > size 712Mb". I have a MacBook Pro with 4Gb of memory. I have been reading > > some posts online, but I haven't found a clear solution. Maybe is a limit > in > > R, or an imposed limit of my system that I should change. Does anyone > knows > > how to do it? Any ideas? > > > > Many thanks, > > > > -- > > Hernando Martínez Vergara > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- Hernando Martínez Vergara [[alternative HTML version deleted]]
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you may also try package xps! steve On Mon, Jun 14, 2010 at 9:57 AM, Hernando Martínez <hernybiotec@gmail.com>wrote: > sorry, I am trying to analize an expression microarray of nearly 350 > samples. My R version is R 2.10.1 GUI 1.31 Leopard build 32-bit (5537). How > do I load R in 64 bit? (maybe this is a trivial question for you but it is > not for me, as I have no computer background). > Thank you very much again, > > Hernando > > 2010/6/14 Benilton Carvalho <beniltoncarvalho@gmail.com> > > > You didn't provide us the information described in the post guide > > (sessionInfo and description of the issue). > > > > R does not impose any limit. > > > > What is the type of array you're trying to analyze? And what > > preprocessing strategy would you like to apply? How many samples do > > you have? Are you using R in 32 or 64 bit mode? > > > > You may be interested in taking a look at justRMA(), if RMA is your > > choice. If you're in 32 bit mode, you definitely want to load R in 64 > > bit... > > > > With more detailed information, we're going to be able to help you out. > > > > b > > > > On 14 June 2010 14:36, Hernando Martínez <hernybiotec@gmail.com> wrote: > > > Hi, I am working with large data, and when I try to read it into R > using > > > 'ReadAffy', I get the following error message: "cannot allocate a > vector > > > size 712Mb". I have a MacBook Pro with 4Gb of memory. I have been > reading > > > some posts online, but I haven't found a clear solution. Maybe is a > limit > > in > > > R, or an imposed limit of my system that I should change. Does anyone > > knows > > > how to do it? Any ideas? > > > > > > Many thanks, > > > > > > -- > > > Hernando Martínez Vergara > > > > > > [[alternative HTML version deleted]] > > > > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > > > -- > Hernando Martínez Vergara > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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FYI: the latest R is 2.11.1, so my recommendation is to upgrade. If you installed R.app (ie, you have R under /Applications) you should have R64.app there too... If you're using the terminal, load R using R --arch x86_64 You will need to reinstall the packages in order to use them in 64 bit. b On 14 June 2010 14:57, Hernando Mart?nez <hernybiotec at="" gmail.com=""> wrote: > sorry, I am trying to analize an expression microarray of nearly 350 > samples. My R version is?R 2.10.1 GUI 1.31 Leopard build 32-bit (5537). How > do I load R in 64 bit? (maybe this is a trivial question for you but it is > not for me, as I have no computer background). > Thank you very much again, > Hernando > > 2010/6/14 Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> >> >> You didn't provide us the information described in the post guide >> (sessionInfo and description of the issue). >> >> R does not impose any limit. >> >> What is the type of array you're trying to analyze? And what >> preprocessing strategy would you like to apply? How many samples do >> you have? Are you using R in 32 or 64 bit mode? >> >> You may be interested in taking a look at justRMA(), if RMA is your >> choice. If you're in 32 bit mode, you definitely want to load R in 64 >> bit... >> >> With more detailed information, we're going to be able to help you out. >> >> b >> >> On 14 June 2010 14:36, Hernando Mart?nez <hernybiotec at="" gmail.com=""> wrote: >> > Hi, I am working with large data, and when I try to read it into R using >> > 'ReadAffy', I get the following error message: "cannot allocate a vector >> > size 712Mb". I have a MacBook Pro with 4Gb of memory. I have been >> > reading >> > some posts online, but I haven't found a clear solution. Maybe is a >> > limit in >> > R, or an imposed limit of my system that I should change. Does anyone >> > knows >> > how to do it? Any ideas? >> > >> > Many thanks, >> > >> > -- >> > Hernando Mart?nez Vergara >> > >> > ? ? ? ?[[alternative HTML version deleted]] >> > >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor at stat.math.ethz.ch >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > > > -- > Hernando Mart?nez Vergara >
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If you're on a mac and you only have 4GB of memory you will likely not get very much additional memory by going 64bit, as the 32bit version is capable of using 3GB and you also need ram for the OS. It is very likely that you will not be ale to run your analysis on your machine. There are 3 possibilities. (1) See if you can get by using justRMA, (2) move to a machine with more RAM, (3) use a package that is designed to run in limited memory like aroma.affymetrix of xps. If you don't have access to a machine with more memory, you should investigate (3). Kasper On Mon, Jun 14, 2010 at 10:01 AM, Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> wrote: > FYI: the latest R is 2.11.1, so my recommendation is to upgrade. > > If you installed R.app (ie, you have R under /Applications) you should > have R64.app there too... > > If you're using the terminal, load R using > > R --arch x86_64 > > You will need to reinstall the packages in order to use them in 64 bit. > > b > > On 14 June 2010 14:57, Hernando Mart?nez <hernybiotec at="" gmail.com=""> wrote: >> sorry, I am trying to analize an expression microarray of nearly 350 >> samples. My R version is?R 2.10.1 GUI 1.31 Leopard build 32-bit (5537). How >> do I load R in 64 bit? (maybe this is a trivial question for you but it is >> not for me, as I have no computer background). >> Thank you very much again, >> Hernando >> >> 2010/6/14 Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> >>> >>> You didn't provide us the information described in the post guide >>> (sessionInfo and description of the issue). >>> >>> R does not impose any limit. >>> >>> What is the type of array you're trying to analyze? And what >>> preprocessing strategy would you like to apply? How many samples do >>> you have? Are you using R in 32 or 64 bit mode? >>> >>> You may be interested in taking a look at justRMA(), if RMA is your >>> choice. If you're in 32 bit mode, you definitely want to load R in 64 >>> bit... >>> >>> With more detailed information, we're going to be able to help you out. >>> >>> b >>> >>> On 14 June 2010 14:36, Hernando Mart?nez <hernybiotec at="" gmail.com=""> wrote: >>> > Hi, I am working with large data, and when I try to read it into R using >>> > 'ReadAffy', I get the following error message: "cannot allocate a vector >>> > size 712Mb". I have a MacBook Pro with 4Gb of memory. I have been >>> > reading >>> > some posts online, but I haven't found a clear solution. Maybe is a >>> > limit in >>> > R, or an imposed limit of my system that I should change. Does anyone >>> > knows >>> > how to do it? Any ideas? >>> > >>> > Many thanks, >>> > >>> > -- >>> > Hernando Mart?nez Vergara >>> > >>> > ? ? ? ?[[alternative HTML version deleted]] >>> > >>> > >>> > _______________________________________________ >>> > Bioconductor mailing list >>> > Bioconductor at stat.math.ethz.ch >>> > https://stat.ethz.ch/mailman/listinfo/bioconductor >>> > Search the archives: >>> > http://news.gmane.org/gmane.science.biology.informatics.conductor >>> > >> >> >> >> -- >> Hernando Mart?nez Vergara >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Thank you all very much. For the moment I can analyze the data using R64. However, I need to analyse as well a bigger matrix, to maybe I will need the other proposed solutions as well. Again, thanks, you have been very helpful. Hernando 2010/6/14 Kasper Daniel Hansen <kasperdanielhansen@gmail.com> > If you're on a mac and you only have 4GB of memory you will likely not > get very much additional memory by going 64bit, as the 32bit version > is capable of using 3GB and you also need ram for the OS. It is very > likely that you will not be ale to run your analysis on your machine. > > There are 3 possibilities. (1) See if you can get by using justRMA, > (2) move to a machine with more RAM, (3) use a package that is > designed to run in limited memory like aroma.affymetrix of xps. > > If you don't have access to a machine with more memory, you should > investigate (3). > > Kasper > > On Mon, Jun 14, 2010 at 10:01 AM, Benilton Carvalho > <beniltoncarvalho@gmail.com> wrote: > > FYI: the latest R is 2.11.1, so my recommendation is to upgrade. > > > > If you installed R.app (ie, you have R under /Applications) you should > > have R64.app there too... > > > > If you're using the terminal, load R using > > > > R --arch x86_64 > > > > You will need to reinstall the packages in order to use them in 64 bit. > > > > b > > > > On 14 June 2010 14:57, Hernando Martínez <hernybiotec@gmail.com> wrote: > >> sorry, I am trying to analize an expression microarray of nearly 350 > >> samples. My R version is R 2.10.1 GUI 1.31 Leopard build 32-bit (5537). > How > >> do I load R in 64 bit? (maybe this is a trivial question for you but it > is > >> not for me, as I have no computer background). > >> Thank you very much again, > >> Hernando > >> > >> 2010/6/14 Benilton Carvalho <beniltoncarvalho@gmail.com> > >>> > >>> You didn't provide us the information described in the post guide > >>> (sessionInfo and description of the issue). > >>> > >>> R does not impose any limit. > >>> > >>> What is the type of array you're trying to analyze? And what > >>> preprocessing strategy would you like to apply? How many samples do > >>> you have? Are you using R in 32 or 64 bit mode? > >>> > >>> You may be interested in taking a look at justRMA(), if RMA is your > >>> choice. If you're in 32 bit mode, you definitely want to load R in 64 > >>> bit... > >>> > >>> With more detailed information, we're going to be able to help you out. > >>> > >>> b > >>> > >>> On 14 June 2010 14:36, Hernando Martínez <hernybiotec@gmail.com> > wrote: > >>> > Hi, I am working with large data, and when I try to read it into R > using > >>> > 'ReadAffy', I get the following error message: "cannot allocate a > vector > >>> > size 712Mb". I have a MacBook Pro with 4Gb of memory. I have been > >>> > reading > >>> > some posts online, but I haven't found a clear solution. Maybe is a > >>> > limit in > >>> > R, or an imposed limit of my system that I should change. Does anyone > >>> > knows > >>> > how to do it? Any ideas? > >>> > > >>> > Many thanks, > >>> > > >>> > -- > >>> > Hernando Martínez Vergara > >>> > > >>> > [[alternative HTML version deleted]] > >>> > > >>> > > >>> > _______________________________________________ > >>> > Bioconductor mailing list > >>> > Bioconductor@stat.math.ethz.ch > >>> > https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> > Search the archives: > >>> > http://news.gmane.org/gmane.science.biology.informatics.conductor > >>> > > >> > >> > >> > >> -- > >> Hernando Martínez Vergara > >> > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- Hernando Martínez Vergara [[alternative HTML version deleted]]
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