[BioC] Wow, what have I done

[Loren Engrav]

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