Hello, I am running some microarray analysis data and am using the rma function. I have to read more than 100 files of 10MB each as a group and use rma function over all of these . I am trying to read those but it is giving me memory allocation probem. I have increased the memory using the memory.limit(size=) however it is still giving error that it cannot allocate vector. Please guide me on what I can do to avoid this problem. Regards, Tapan Mehta

Hello, I am running some microarray analysis data and am using the rma function. I have to read more than 100 files of 10MB each as a group and use rma function over all of these . I am trying to read those but it is giving me memory allocation probem. I have increased the memory using the memory.limit(size=) however it is still giving error that it cannot allocate vector. Please guide me on what I can do to avoid this problem. Following is the error Data<-ReadAffy() Error: cannot allocate vector of size 174400 Kb In addition: Warning message: Reached total allocation of 255Mb: see help(memory.size) > memory.limit(size=180000) NULL > Data<-ReadAffy() Error: cannot allocate vector of size 174400 Kb > Please guide me Regards, Tapan Mehta

So do you have a computer with 1 or 2 Gb memory? Are you running Windows or Linux? Tapan Mehta <tapmehta@yahoo.com> writes: > I am running some microarray analysis data and am > using the rma function. I have to read more than 100 > files of 10MB each as a group and use rma function > over all of these . I am trying to read those but it > is giving me memory allocation probem. I have > increased the memory using the memory.limit(size=) > however it is still giving error that it cannot > allocate vector. Please guide me on what I can do to > avoid this problem. > > Following is the error > > Data<-ReadAffy() > Error: cannot allocate vector of size 174400 Kb > In addition: Warning message: > Reached total allocation of 255Mb: see > help(memory.size) >> memory.limit(size=180000) > NULL >> Data<-ReadAffy() > Error: cannot allocate vector of size 174400 Kb >> > > > Please guide me > > Regards, > > Tapan Mehta > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > -- A.J. Rossini rossini@u.washington.edu http://software.biostat.washington.edu/ Biostatistics, U Washington and Fred Hutchinson Cancer Research Center FHCRC:Tu: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email UW : Th: 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX CONFIDENTIALITY NOTICE: This e-mail message and any attachments ... {{dropped}}

You have set too low amount of memory: 174000 Kb ~ 170Mb, your files=100*10Mb~1Gb Try with memory.limit(size=1024M). If you work on MSWin platform is better --max-mem-size (flag for command R-term or R-gui). Good job! A.S. ---------------------------- Alessandro Semeria Models and Simulations Laboratory The Environment Research Center - Montecatini (Edison Group), Via Ciro Menotti 48, 48023 Marina di Ravenna (RA), Italy Tel. +39 544 536811 Fax. +39 544 538663 E-mail: asemeria@cramont.it