[BioC] Memory Requirments

[Robert Gentleman]

Hi,
  two (and a half) points,

  please indicate what platform and what version of R you are using -
  it is hard to give good advice without you giving us some
  indications 

  it looks like Windows, in that case there is a FAQ that you can look
  at (www.r-project.org) and the mailing list archives have a number
  of discussions of just this point, please have a look there

  memory usage with affy (and a few other things) has been an issue,
  we are trying to address it and I think that things should improve
  shortly. Manually removing unneeded objects might help as well.


  Robert

On Wed, Jun 25, 2003 at 08:56:12AM -0400, Michael Barnes wrote:
> What are the memory requirments when running Bioconductor's Affy
> package?  I have 38 U95a chips and when I try to process the data I
> get:
> 
>  expresso(Data,widget=TRUE)
> background correction: rma 
> normalization: quantiles 
> PM/MM correction : pmonly 
> expression values: medianpolish 
> background correcting...Error: cannot allocate vector of size 83200 Kb
> In addition: Warning message: 
> Reached total allocation of 1024Mb: see help(memory.size) 
> 
> Is this saying that the vector size for each chip is 83Mb?  Otherwise,
> what is going on?
> 
> In addition, is this a reasonable analysis or is this duplicating the
> functions used in rma as may be suggested in "Textual description of
> Affy", pg 14?  I don't quite understand from the vignette.
> 
> Michael Barnes
> 
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| Robert Gentleman                 phone : (617) 632-5250                   |
| Associate Professor              fax:   (617)  632-2444                   |
| Department of Biostatistics      office: M1B20                            |
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