Hi I've recently downloaded R 2.10.0 to analyse microarray data with affyGUI and following the instructions online (Estrogen example data set) downloaded the additional getBioC, tkrplot and ActiveTC 8.5.8.0. When I try to upload my unzipped cel files I get an error message: An error has occurred Cannot allocate vector of size 600.0 Mb Error in assign("RawAffyData" , RawAffyData, affylmGUIenvironment) : object 'RawAffyData' not found Error in exprs(RawAffyData) : Error in evaluating the argument 'object' in selecting a method for function 'exprs' The data is shown as available and the RNA target file is correct but when I try to analyse it, for example intensity density plots I get further error messages: Error in function (classes, fdef, mtable) ; Unable to find an inherited method for function "indexProbes", for signature "numeric", "character" Error in strwidth(legend, units = "user", cex = cex): Plot.new has not been called yet Error in title(plotTitle) : plot.new has not been called yet Further error messages in the R console also appear: In addition: Warning messages: 1: In dimnames(x) <- dn : Reached total allocation of 758Mb: see help(memory.size) Is there a simple way I can fix this? Apologies if I'm missing something obvious, it's a very new subject for me and I can't find an answer online! Thanks, Christine

Hi Christine, Christine Tomlins wrote: > Hi > I've recently downloaded R 2.10.0 to analyse microarray data with affyGUI and following the instructions online (Estrogen example data set) downloaded the additional getBioC, tkrplot and ActiveTC 8.5.8.0. > When I try to upload my unzipped cel files I get an error message: > > An error has occurred > Cannot allocate vector of size 600.0 Mb This error indicates that you don't have enough RAM to process all the data. You may be able to free up enough RAM by closing other programs that you have running. If that doesn't work, you will likely need to increase the amount of RAM in your computer, or use a different computer that has sufficient RAM to do the analysis. Best, Jim > Error in assign("RawAffyData" , RawAffyData, affylmGUIenvironment) : object 'RawAffyData' not found > Error in exprs(RawAffyData) : > Error in evaluating the argument 'object' in selecting a method for function 'exprs' > > The data is shown as available and the RNA target file is correct but when I try to analyse it, for example intensity density plots I get further error messages: > > Error in function (classes, fdef, mtable) ; > Unable to find an inherited method for function "indexProbes", for signature "numeric", "character" > Error in strwidth(legend, units = "user", cex = cex): > Plot.new has not been called yet > Error in title(plotTitle) : plot.new has not been called yet > > Further error messages in the R console also appear: > > In addition: Warning messages: > 1: In dimnames(x) <- dn : > Reached total allocation of 758Mb: see help(memory.size) > > Is there a simple way I can fix this? Apologies if I'm missing something obvious, it's a very new subject for me and I can't find an answer online! > Thanks, > Christine > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

>Message: 17 >Date: Thu, 14 Jan 2010 13:14:46 -0500 >From: "James W. MacDonald" <jmacdon at="" med.umich.edu=""> >To: Christine Tomlins <christine.tomlins at="" linacre.ox.ac.uk=""> >Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> >Subject: Re: [BioC] affylmGUI .cel loading problem >Message-ID: <4B4F5F16.5010404 at med.umich.edu> >Content-Type: text/plain; charset="iso-8859-1"; format="flowed" Hi Christine, >Christine Tomlins wrote: > > Hi > > I've recently downloaded R 2.10.0 to analyse microarray data with affyGUI and following the instructions online (Estrogen example data set) downloaded the additional getBioC, tkrplot and ActiveTC 8.5.8.0. > > When I try to upload my unzipped cel files I get an error message: > > > > An error has occurred > > Cannot allocate vector of size 600.0 Mb > If you are using windows based computer, if you have little RAM you can swap to the HD, off course this will reduce the over all speed of the analysis. Go in the propriety of the R ICON and change YourDisk:SomewhereInYourDisk\R\R-2.10.0\bin\Rgui.exe with YourDisk:SomewhereInYourDisk\R\R-2.10.0\bin\Rgui.exe --max-mem- size=2047M Cheers Raffaele -- ---------------------------------------- Prof. Raffaele A. Calogero Bioinformatics and Genomics Unit Dipartimento di Scienze Cliniche e Biologiche Az. Ospedaliero-Universitaria S. Luigi Regione Gonzole 10, Orbassano 10043 Torino tel. ++39 0116705417 Lab. ++39 0116705408 Fax ++39 0119038639 Mobile ++39 3333827080 email: raffaele.calogero at unito.it raffaele[dot]calogero[at]gmail[dot]com www: http://www.bioinformatica.unito.it Info: http://publicationslist.org/raffaele.calogero