Hi! New to this list and to Bioconductor, I apologize if bringing up old matters, but I need a solution to my problem, which is: When trying to load a set of 30 x (hgu133_plus_2) .cel files, this message pops up: > rawBcells<-ReadAffy() Error: cannot allocate vector of size 317553 Kb In addition: Warning message: Reached total allocation of 1022Mb: see help(memory.size) Obviously there is a shortage of memory as I interpret it. So, any suggestions on how I should address this, since I want to run gcrma, normalizations and clustering etc on this set? The next problem arising is when trying to run separate files with gcrma: > raw0001<-ReadAffy("B cells P-00.01.CEL") > grma0001<-gcrma(raw0001) Computing affinities.Done. Adjusting for optical effect.Done. Error in model.frame(formula, rownames, variables, varnames, extras, extranames, : variable lengths differ is gcrma unable to read (hgu133_plus_2).cel files? The library for hgu133_plus_2 is loaded OK. Thanks! Carl-Magnus

Carl-Magnus, Does justGCRMA work for you? I don't use it, but my understanding is that it helps to deal with some of the memory issues with the multistep solution. The answers you get are the same, again, as I understand it. Others may have more to say on the matter. Sean On Jan 25, 2005, at 9:26 AM, Carl-Magnus H?gerkorp wrote: > Hi! > > New to this list and to Bioconductor, I apologize if bringing up old > matters, but I need a solution to my problem, which is: > > When trying to load a set of 30 x (hgu133_plus_2) .cel files, this > message > pops up: > >> rawBcells<-ReadAffy() > Error: cannot allocate vector of size 317553 Kb > In addition: Warning message: > Reached total allocation of 1022Mb: see help(memory.size) > > Obviously there is a shortage of memory as I interpret it. > So, any suggestions on how I should address this, since I want to run > gcrma, > normalizations and clustering etc on this set? > > The next problem arising is when trying to run separate files with > gcrma: > >> raw0001<-ReadAffy("B cells P-00.01.CEL") >> grma0001<-gcrma(raw0001) > Computing affinities.Done. > Adjusting for optical effect.Done. > Error in model.frame(formula, rownames, variables, varnames, extras, > extranames, : > variable lengths differ > > is gcrma unable to read (hgu133_plus_2).cel files? > The library for hgu133_plus_2 is loaded OK. > > Thanks! > > Carl-Magnus > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor

Carl-Magnus H?gerkorp wrote: > Hi! > > New to this list and to Bioconductor, I apologize if bringing up old > matters, but I need a solution to my problem, which is: > > When trying to load a set of 30 x (hgu133_plus_2) .cel files, this message > pops up: > > >>rawBcells<-ReadAffy() > > Error: cannot allocate vector of size 317553 Kb > In addition: Warning message: > Reached total allocation of 1022Mb: see help(memory.size) > > Obviously there is a shortage of memory as I interpret it. > So, any suggestions on how I should address this, since I want to run gcrma, > normalizations and clustering etc on this set? You could try justGCRMA(), which uses much less memory. Alternatively you could purchase another Gig of RAM, which these days is very inexpensive. > > The next problem arising is when trying to run separate files with gcrma: > > >>raw0001<-ReadAffy("B cells P-00.01.CEL") >>grma0001<-gcrma(raw0001) > > Computing affinities.Done. > Adjusting for optical effect.Done. > Error in model.frame(formula, rownames, variables, varnames, extras, > extranames, : > variable lengths differ > > is gcrma unable to read (hgu133_plus_2).cel files? > The library for hgu133_plus_2 is loaded OK. No, it is because you tried to run gcrma on only one chip. For any of the methods that model the probe-level data (gcrma, rma, affyPLM, li.wong), it doesn't make any sense to use only one chip, which is why you are erroring out. Try using maybe 4 or 5 chips and see what happens. > > Thanks! > > Carl-Magnus > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109

I guess that you can try something like: >memory.limit(size=1500) or whatever size you like. If you have a slow computer and a lot of data, you might have to wait for a long long time.. :) Marcus Gry Bj?rklund Royal Institute of Technology AlbaNova University Center Department of Molecular Biotechnology 106 91 Stockholm, Sweden Phone (office): +46 8 553 783 44 Fax: + 46 8 553 784 81 Visiting address: Roslagstullsbacken 21, Floor 3 Delivery address: Roslagsv?gen 30B Web: http://www.biotech.kth.se/molbio/microarray/index.html -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Carl- Magnus H?gerkorp Sent: Tuesday, January 25, 2005 15:26 To: Bioconductor Subject: [BioC] hgu133_plus_2? Hi! New to this list and to Bioconductor, I apologize if bringing up old matters, but I need a solution to my problem, which is: When trying to load a set of 30 x (hgu133_plus_2) .cel files, this message pops up: > rawBcells<-ReadAffy() Error: cannot allocate vector of size 317553 Kb In addition: Warning message: Reached total allocation of 1022Mb: see help(memory.size) Obviously there is a shortage of memory as I interpret it. So, any suggestions on how I should address this, since I want to run gcrma, normalizations and clustering etc on this set? The next problem arising is when trying to run separate files with gcrma: > raw0001<-ReadAffy("B cells P-00.01.CEL") > grma0001<-gcrma(raw0001) Computing affinities.Done. Adjusting for optical effect.Done. Error in model.frame(formula, rownames, variables, varnames, extras, extranames, : variable lengths differ is gcrma unable to read (hgu133_plus_2).cel files? The library for hgu133_plus_2 is loaded OK. Thanks! Carl-Magnus _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor