Hello. Might someone have a solution to this problem? > aricAffy6<-read.plink('ARIC_CARe_Affy6_FINAL_2989.bed') Number of SNPs: 796384 SNP_A-8282315 SNP_A-8282317 SNP_A-8289954 SNP_A-8289982 SNP_A-8289994 SNP_A-8338 245 ... Number of samples: 2989 1I5D8C DLAJ5B 3OW97U S4EL8O 8N5Z18 7AXAF7 ... Error in read.plink("ARIC_CARe_Affy6_FINAL_2989.bed") : allocMatrix: too many elements specified > mem.limits() nsize vsize NA NA $ free -m total used free shared buffers cached Mem: 64396 48317 16079 0 397 46126 -/+ buffers/cache: 1793 62603 Swap: 1983 0 1983 Thanks, Jim ------------------------------------------------------ > R.Version() $platform [1] "x86_64-redhat-linux-gnu" $arch [1] "x86_64" $os [1] "linux-gnu" $system [1] "x86_64, linux-gnu" $status [1] "" $major [1] "2" $minor [1] "8.1" $year [1] "2008" $month [1] "12" $day [1] "22" $`svn rev` [1] "47281" $language [1] "R" $version.string [1] "R version 2.8.1 (2008-12-22)" [[alternative HTML version deleted]]

i believe you have tried to cross a fundamental limit to vector size in R. > 796384*2989 [1] 2380391776 > log2(.Last.value) [1] 31.14855 Break the snp data up by chromosomes and manage, perhaps, in a list. or exclude some samples. On Fri, Sep 24, 2010 at 12:49 PM, Jim Moon <moonja at="" ohsu.edu=""> wrote: > Hello. ?Might someone have a solution to this problem? > >> aricAffy6<-read.plink('ARIC_CARe_Affy6_FINAL_2989.bed') > Number of SNPs: ?796384 > SNP_A-8282315 SNP_A-8282317 SNP_A-8289954 SNP_A-8289982 SNP_A-8289994 SNP_A-8338 > 245 ?... > Number of samples: ?2989 > 1I5D8C DLAJ5B 3OW97U S4EL8O 8N5Z18 7AXAF7 ... > Error in read.plink("ARIC_CARe_Affy6_FINAL_2989.bed") : > ?allocMatrix: too many elements specified > >> mem.limits() > nsize vsize > ? NA ? ?NA > > $ free -m > ? ? ? ? ? ? total ? ? ? used ? ? ? free ? ? shared ? ?buffers ? ? cached > Mem: ? ? ? ? 64396 ? ? ?48317 ? ? ?16079 ? ? ? ? ?0 ? ? ? ?397 ? ? ?46126 > -/+ buffers/cache: ? ? ? 1793 ? ? ?62603 > Swap: ? ? ? ? 1983 ? ? ? ? ?0 ? ? ? 1983 > > > Thanks, > Jim > > ------------------------------------------------------ >> R.Version() > $platform > [1] "x86_64-redhat-linux-gnu" > $arch > [1] "x86_64" > $os > [1] "linux-gnu" > $system > [1] "x86_64, linux-gnu" > $status > [1] "" > $major > [1] "2" > $minor > [1] "8.1" > $year > [1] "2008" > $month > [1] "12" > $day > [1] "22" > $`svn rev` > [1] "47281" > $language > [1] "R" > $version.string > [1] "R version 2.8.1 (2008-12-22)" > > ? ? ? ?[[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 >

The issue is that R has this internal limit of 2^31-1 elements per object... and, guess what, 796384*2989 is bigger than 2^31-1. So you probably want to split your BED file in two and try from there... b On 24 September 2010 17:49, Jim Moon <moonja at="" ohsu.edu=""> wrote: > Hello. ?Might someone have a solution to this problem? > >> aricAffy6<-read.plink('ARIC_CARe_Affy6_FINAL_2989.bed') > Number of SNPs: ?796384 > SNP_A-8282315 SNP_A-8282317 SNP_A-8289954 SNP_A-8289982 SNP_A-8289994 SNP_A-8338 > 245 ?... > Number of samples: ?2989 > 1I5D8C DLAJ5B 3OW97U S4EL8O 8N5Z18 7AXAF7 ... > Error in read.plink("ARIC_CARe_Affy6_FINAL_2989.bed") : > ?allocMatrix: too many elements specified > >> mem.limits() > nsize vsize > ? NA ? ?NA > > $ free -m > ? ? ? ? ? ? total ? ? ? used ? ? ? free ? ? shared ? ?buffers ? ? cached > Mem: ? ? ? ? 64396 ? ? ?48317 ? ? ?16079 ? ? ? ? ?0 ? ? ? ?397 ? ? ?46126 > -/+ buffers/cache: ? ? ? 1793 ? ? ?62603 > Swap: ? ? ? ? 1983 ? ? ? ? ?0 ? ? ? 1983 > > > Thanks, > Jim > > ------------------------------------------------------ >> R.Version() > $platform > [1] "x86_64-redhat-linux-gnu" > $arch > [1] "x86_64" > $os > [1] "linux-gnu" > $system > [1] "x86_64, linux-gnu" > $status > [1] "" > $major > [1] "2" > $minor > [1] "8.1" > $year > [1] "2008" > $month > [1] "12" > $day > [1] "22" > $`svn rev` > [1] "47281" > $language > [1] "R" > $version.string > [1] "R version 2.8.1 (2008-12-22)" > > ? ? ? ?[[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 >