[BioC] Wow, what have I done

[cstrato]

Dear Loren

As an alternative you could try package "xps", which I have developed on
my Titanium PowerBook and which works with R-2.6.1.
It is able to handle your 70 HGU133p2 CEL-files with even 1GB RAM only.
However, it supplies RMA and MAS5 only but not GCRMA.

Regards
Christian
_._._._._._._._._._._._._._._._
C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a
V.i.e.n.n.a A.u.s.t.r.i.a
e.m.a.i.l: cstrato at aon.at
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Loren Engrav wrote:
> Thank you all and sorry for the unclear subject
>
> I did get down to this in the documentation..........
>
> Depending on the size of your dataset and on the memory available to your
> system, you might experience errors like ŒCannot allocate vector . . . ¹. An
> obvious option is to increase the memory available to your R process (by
> adding memory and/or closing external applications2 . An another option is
> to use the function justRMA. (or explore ulimit)
> R> eset <- justRMA()
> This reads the data and performs the ŒRMA¹ way to preprocess them at the C
> level. One does not need to call ReadAffy, probe level data is never stored
> in an AffyBatch. rma continues to be the recommended function for computing
> RMA.
>
> So...
> I tried killing other processes and it went a little further but then failed
> with same message
>
> I then tried
>   
>> library(affy)
>> library(hgu133plus2cdf)
>> GibranGlue81 <- justRMA() #load 81 .cel files
>>     
>
> And it returned
> Background correcting
> Error in density.default(x, kernel = "epanechnikov", n = 2^14) :
>   need at least 2 points to select a bandwidth automatically
>
> And most of our previous stuff is gcrma and not sure mixing is a good idea
> if this is mixing
>
> And finally as per the documentation I examined "ulimit", but that might be
> a little aggressive for me at this point given my knowledge of unix
>
> Again
>   
>> sessionInfo()
>>     
> R version 2.6.1 (2007-11-26)
> powerpc-apple-darwin8.10.1
>
> locale:
> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> base     
>
> other attached packages:
> [1] hgu133plus2cdf_2.0.0 affy_1.16.0          preprocessCore_1.0.0
> affyio_1.6.1         Biobase_1.16.1
>   
>
> Thank you again for the help
>
> Loren Engrav
> Univ Washington
> Seattle
>
>
>
>
>
>
> From: Sean Davis <sdavis2 at mail.nih.gov>
> Date: Sat, 8 Dec 2007 07:49:36 -0500
> To: Loren Engrav <engrav at u.washington.edu>
> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
> Subject: Re: [BioC] Wow, what have I done
>
>
>
> On Dec 8, 2007 1:00 AM, Loren Engrav <engrav at u.washington.edu> wrote:
>   
>> Ok
>> SessionInfo now returns
>>
>>     
>>> sessionInfo()
>>>       
>> R version 2.6.1 (2007-11-26)
>> powerpc-apple-darwin8.10.1
>>
>> locale:
>> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] tools     stats     graphics  grDevices utils     datasets  methods
>> base
>>
>> other attached packages:
>> [1] affy_1.16.0          preprocessCore_1.0.0 affyio_1.6.1
>> Biobase_1.16.1 
>>
>> But I still get
>>     
>>> Gibran70 <- ReadAffy()
>>>       
>> Error: cannot allocate vector of size 723.6 Mb
>> Although not big red messages which is not quite so hostile
>>
>> I guess time to go to bed and in the AM buy some RAM
>>
>> Thank you so much for the help
>>
>> Engrav
>>
>>
>>     
>>> From: Benilton Carvalho <bcarvalh at jhsph.edu>
>>> Date: Sat, 8 Dec 2007 00:23:10 -0500
>>> To: Loren Engrav <engrav at u.washington.edu>
>>> Cc: "bioconductor at stat.math.ethz.ch  <mailto:bioconductor at stat.math.ethz.ch>
>>> " <bioconductor at stat.math.ethz.ch>
>>> Subject: Re: [BioC] Wow, what have I done
>>>
>>> In that case, assuming that R-2.6.1 behaves just like R-2.6.0-patched
>>> in terms of memory management, you might want to define beforehand
>>> what you're going to be doing and, probably, use functions like
>>> justRMA().
>>>       
>
>
> Hi, Loren.  I would really consider following the advice that Benilton gave
> you and use justRMA().  The reason justRMA() was created in the first place
> was to solve the memory problem that you are describing.  I didn't see that
> you had tried this yet (but I might be mistaken), so I just wanted to remind
> you to try it.  If justRMA() will not work for your particular application
> for some reason, it is probably worth outlining for us what you want to do,
> as it may not be necessary to load all the arrays at once to accomplish the
> task. 
>
> In the end, you may want to buy RAM for other reasons, but I think a
> solution might have been proposed already for your current problem.
>
> Sean
>
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