I am attempiting to use the cond.norm function in the smida package to normalise 30 cDNA dual channel arrays with approximately 15000 spots per array. I chose the quantile function using and invariant set =100. Unfortunately I keep getting the following error message "Error: cannot allocate vector of size 207900 Kb". does anyone know what this means? Kind regards Sally Sally-Ann Walford Dept. Molecular and Cell Biology UCT

Sally-Ann Walford <sally at="" science.uct.ac.za=""> writes: > I am attempiting to use the cond.norm function in the smida package to > normalise 30 cDNA dual channel arrays with approximately 15000 spots per > array. I chose the quantile function using and invariant set =100. > Unfortunately I keep getting the following error message "Error: cannot > allocate vector of size 207900 Kb". does anyone know what this > means? It means you are running out of memory. If you have another system to try this on that has more RAM, you may find that your computation succeeds without problem. + seth

It means that your computer is not allocating enough memory to R to do the computation. This is a frequent occurrence on Windows machines. --Naomi At 08:47 AM 4/26/2006, Sally-Ann Walford wrote: >I am attempiting to use the cond.norm function in the smida package to >normalise 30 cDNA dual channel arrays with approximately 15000 spots per >array. I chose the quantile function using and invariant set =100. >Unfortunately I keep getting the following error message "Error: cannot >allocate vector of size 207900 Kb". does anyone know what this means? > >Kind regards >Sally > >Sally-Ann Walford >Dept. Molecular and Cell Biology >UCT > >_______________________________________________ >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 Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111

Sally, I am assuming you are using R/bioc installed in a 32bit Windows envoroment? If so, the largest amount of memory that can physically be accessed is 4Gb (whether that is "proper" RAM or a pagefile on disk). The only way you can get more than that is to get a 64bit computer, or as Seth suggests, use a different operating system that doesn't have the tedious constraints that the Windows OS does. To tell R you want to use as much RAM as possible in a 32bit Windoze enviroment, just type: memory.limit(size=4000) at the beginning of whatever you are trying to do (i.e. on opening the session) (or put it in Rprofile). This is what I get (R2.3.0, Windows GUI): > memory.limit(size=4000) NULL > memory.limit() [1] 4194304000 The pagefile manager within windows will deal with the rest. It does, of course, assume that the total of virtual and physical RAM can get as high as 4Gb (i.e. you have that amount of disk space + installed RAM)! No guarantees, but it should help. a > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of > Sally-Ann Walford > Sent: 26 April 2006 13:48 > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] invariant set normalisation > > > I am attempiting to use the cond.norm function in the smida > package to normalise 30 cDNA dual channel arrays with > approximately 15000 spots per array. I chose the quantile > function using and invariant set =100. > Unfortunately I keep getting the following error message > "Error: cannot allocate vector of size 207900 Kb". does > anyone know what this means? > > Kind regards > Sally > > Sally-Ann Walford > Dept. Molecular and Cell Biology > UCT > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/biocondu> ctor > Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >