Restatement: Was Re: [BioC] Memory Requirments

[Michael Barnes]

This is in response to the various answers I received to my questions
below.  First, thank you all for your comments about duplicating work
with the command I used.  Secondly, I am running Windows XP with R
1.7.1.

I should point out that according to the May 15th posting, Laurent
Gautier's method does not run on Windows.

I would also like to point out that I had already visited the FAQs and
the past posing for this list before my current posting and tried
?memroy.size.  

I have sucessfully run this analysis using rma, so I would assume
justRMA should work too.  However, as my questions below will show, I am
concerned about how to determine the amount of memory I will need in the
future.

I apparently did not make my question specific enough.  So...  

I know how to check the memory and have increased the memory already. 
My two questions are:  

1.  Concerning the error below, 83200kb is less than the allocated 1024
Mb.  Does this mean that it requires 83200Kb for each chip (ie I need
83200kb for each of 38 chips or a total of about 3000 Mb) or does this
mean that there are other memory usages that are causing this memory
issue?  ie, is this due to the data processing for the analysis I have
tried to perform?

2.  Sort of the reverse of that question, is there an estimate for the
amount of memory needed based on the number of chips being analyzed?  I
could go to another computer, buy more memory, or something else, but
what do I need in order to be able to do the analysis that I want here
or I might chose to do in the future?  Is there some way to approximate
these requirements?  This is assuming I wanted to use rma (or an
estimate for justRMA would be good too).  If I decide later that I want
to use one of the other analyses in Affy, is there some way, other than
trial and error, to guess/approximate the amount of memory I will need?

Thank you all,

Michael Barnes


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
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch 
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor 

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