[BioC] affylmGUI .cel loading problem

Christine Tomlins christine.tomlins at linacre.ox.ac.uk
Wed Jan 13 18:59:56 CET 2010

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
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!

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