Dear Daniel As Vincent already mentioned, one alternative is package xps, which can easily handle many exon CEL-files on computers with 1 GB RAM only (another alternative would be package aroma.affymetrix). Best regards Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._ Vincent Carey wrote: > it looks like 10GB is simply not enough. on a fairly large machine i just read > 33 _mouse_ exon 1.0 st arrays using oligo::read.celfiles and noted that the > memory consumption did rise above 10GB (but not by much) after parsing. > > you didn't include your sessionInfo() output but that could be useful. > > it remains to be seen whether one could profitably chop up the parsing > with oligo > into blocks and then combine the results into something useful given this > RAM limitation. other approaches for these arrays include exonmap and xps > but illustration of a complete oligo-based workflow for these arrays > should be forthcoming > soon > > On Tue, Jun 23, 2009 at 6:17 AM, Daniel Brewer<daniel.brewer at="" icr.ac.uk=""> wrote: > >> Just trying out the oligo package on some Human Exon 1.0 ST microarrays >> and I get an error while doing a read.celfiles. I am running OS X >> Leopard on a macpro with 10GB memory. >> >> >>> yoda <- read.celfiles(list.celfiles("CEL",full.names=T)) >>> >> Platform design info loaded. >> Reading in : CEL/1208_CoC(3)25_ExH_PRC125.CEL >> Reading in : CEL/1208_CoC(3)26_ExH_PRC126.CEL >> Reading in : CEL/1208_CoC(3)27_ExH_PRC127.CEL >> Reading in : CEL/1208_CoC(3)28_ExH_PRC128.CEL >> Reading in : CEL/1208_CoC(3)29_ExH_PRC129.CEL >> Reading in : CEL/1208_CoC(3)30_ExH_PRC130.CEL >> Reading in : CEL/1208_CoC(3)31_ExH_NP1.CEL >> Reading in : CEL/1208_CoC(3)32_ExH_NP2.CEL >> Reading in : CEL/1208_CoC(3)33_ExH_NP3.CEL >> Reading in : CEL/1208_CoC(3)34_ExH_NP4.CEL >> Reading in : CEL/1208_CoC(3)35_ExH_NP5.CEL >> Reading in : CEL/1208_CoC(3)36_ExH_NP6.CEL >> Reading in : CEL/1208_CoC(3)37_ExH_NP7.CEL >> Reading in : CEL/1208_CoC(3)38_ExH_ST1.CEL >> R(2640) malloc: *** mmap(size=734007296) failed (error code=12) >> *** error: can't allocate region >> *** set a breakpoint in malloc_error_break to debug >> R(2640) malloc: *** mmap(size=734007296) failed (error code=12) >> *** error: can't allocate region >> *** set a breakpoint in malloc_error_break to debug >> Error: cannot allocate vector of size 700.0 Mb >> >> >> Any ideas whats going on? >> >> Dan >> >> -- >> ************************************************************** >> Daniel Brewer, Ph.D. >> >> Institute of Cancer Research >> Molecular Carcinogenesis >> Email: daniel.brewer at icr.ac.uk >> ************************************************************** >> >> The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. >> >> This e-mail message is confidential and for use by the a...{{dropped:2}} >> >> _______________________________________________ >> 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 >> >> > > > >

Doh. That gives 4, looks like I am running the 32bit version. Off to look for a 64bit binary. Thanks Dan Tobias Straub wrote: > Hi Dan, > > are you running 64bit R? > what's your output of .Machine$sizeof.pointer > > Tobias > > On Jun 23, 2009, at 12:17 PM, Daniel Brewer wrote: > >> Just trying out the oligo package on some Human Exon 1.0 ST microarrays >> and I get an error while doing a read.celfiles. I am running OS X >> Leopard on a macpro with 10GB memory. >> >>> yoda <- read.celfiles(list.celfiles("CEL",full.names=T)) >> Platform design info loaded. >> Reading in : CEL/1208_CoC(3)25_ExH_PRC125.CEL >> Reading in : CEL/1208_CoC(3)26_ExH_PRC126.CEL >> Reading in : CEL/1208_CoC(3)27_ExH_PRC127.CEL >> Reading in : CEL/1208_CoC(3)28_ExH_PRC128.CEL >> Reading in : CEL/1208_CoC(3)29_ExH_PRC129.CEL >> Reading in : CEL/1208_CoC(3)30_ExH_PRC130.CEL >> Reading in : CEL/1208_CoC(3)31_ExH_NP1.CEL >> Reading in : CEL/1208_CoC(3)32_ExH_NP2.CEL >> Reading in : CEL/1208_CoC(3)33_ExH_NP3.CEL >> Reading in : CEL/1208_CoC(3)34_ExH_NP4.CEL >> Reading in : CEL/1208_CoC(3)35_ExH_NP5.CEL >> Reading in : CEL/1208_CoC(3)36_ExH_NP6.CEL >> Reading in : CEL/1208_CoC(3)37_ExH_NP7.CEL >> Reading in : CEL/1208_CoC(3)38_ExH_ST1.CEL >> R(2640) malloc: *** mmap(size=734007296) failed (error code=12) >> *** error: can't allocate region >> *** set a breakpoint in malloc_error_break to debug >> R(2640) malloc: *** mmap(size=734007296) failed (error code=12) >> *** error: can't allocate region >> *** set a breakpoint in malloc_error_break to debug >> Error: cannot allocate vector of size 700.0 Mb >> >> >> Any ideas whats going on? >> >> Dan >> >> -- >> ************************************************************** >> Daniel Brewer, Ph.D. >> >> Institute of Cancer Research >> Molecular Carcinogenesis >> Email: daniel.brewer at icr.ac.uk >> ************************************************************** >> >> The Institute of Cancer Research: Royal Cancer Hospital, a charitable >> Company Limited by Guarantee, Registered in England under Company No. >> 534147 with its Registered Office at 123 Old Brompton Road, London SW7 >> 3RP. >> >> This e-mail message is confidential and for use by the a...{{dropped:2}} >> >> _______________________________________________ >> 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 > > ---------------------------------------------------------------------- > Tobias Straub ++4989218075439 Adolf-Butenandt-Institute, M?nchen D > > > > -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis MUCRC 15 Cotswold Road Sutton, Surrey SM2 5NG United Kingdom Tel: +44 (0) 20 8722 4109 ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the a...{{dropped:2}}