[BioC] affylmGUI .cel loading problem

James W. MacDonald jmacdon at med.umich.edu
Thu Jan 14 19:14:46 CET 2010

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  
> 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.



> 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
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James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
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