[BioC] BGX Output Help

[Kasper Daniel Hansen]

On Jan 16, 2008, at 5:03 AM, Louisa A Rispoli/AS/EXP/UTIA wrote:

> hits=-2.6 tests=BAYES_00
> X-USF-Spam-Flag: NO
>
>
> To all-
>
> I know that I am having a problem with memory based on the error  
> that I
> just received but I cannot figure out how the issue is happening. I  
> ran the
> bgx analysis without issue but when try to get the output analyzed  
> I am
> receiving an error "Error: cannot allocate vector of size 188.5 Mb"  
> on a
> maching that has 2.0 GB of RAM. Any suggestions?

All you can tell from this error message is that you are missing ram.  
Say you are in the situation that you are using 1.9 GB and then try  
to create an object of 200MB. Then the error will be "cannot allocate  
vector of size 200MB", so you are probably using way more memory.

It seems like you are reading in some big output files. This may be  
made possible by changing the reading routine to a function that is  
less memory hungry. Or you might simply have to little RAM. I suggest  
contacting the authors of BGX. It seems pretty silly that an output  
analysis of a MCMC run stored on disk should be so memory hungry - of  
course that depends on what they are doing.

Kasper


> Thanks
>
> Louisa Rispoli
>
>
>> library(bgx)
> Loading required package: Biobase
> Loading required package: tools
>
> Welcome to Bioconductor
>
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Loading required package: affy
> Loading required package: affyio
> Loading required package: preprocessCore
> Loading required package: gcrma
> Loading required package: matchprobes
> Loading required package: splines
> Warning message:
> package 'bgx' was built under R version 2.6.1
>> WTData <- ReadAffy()
>> WTeset <- bgx(WTData, samplesets = c(3,3), output="minimal")
> Analyse 6 array(s) in 2 condition(s):
>         - condition 1: 3 array(s)
>         - condition 2: 3 array(s)
> Analyse all genes
> Take into account probe affinities (threshold is  100  probes per  
> category)
> Computing affinities.Done.
> There are  69  probe affinity categories
> There are  0  probes with no sequence information (initial category  
> set to
> median)
> Warning: There were 45 probe sets with PM<=MM for all probes.
> Starting MCMC simulation...
> 8192 burn-in sweeps completed.
> 16384 sampling sweeps completed.
> MCMC duration: 7h 15m 0s
> CEL files analysed:     WTampC_rep1.cel, WTampC_rep2.cel,  
> WTampC_rep3.cel,
> WTampM_rep1.cel, WTampM_rep2.cel, WTampM_rep3.cel
> Results are in ./run.3
> Run finished.
>> bgxOutput <- readOutput.bgx("run.3")
> Reading 'run.3'
> *** Number of samples:
>     6
> *** Number of conditions:
>     2
> *** Number of probes:
>     265627
> *** Number of genes:
>     24128
> *** Number of categories:
>     69
> *** Number of probes with no sequence information:
>     0
> *** Number of genes to monitor fully:
>     0
> *** Subsampling interval:
>     16
> *** Number of burn-in sweeps:
>     8192
> *** Number of sampling sweeps:
>     16384
> *** Spread of jumps in S:
>     30
> *** Spread of jumps in H:
>     350
> *** Spread of jumps in mu:
>     1.1
> *** Spread of jumps in sigma:
>     1.5
> *** Spread of jumps in lambda:
>     0.04
> *** Spread of jumps in eta:
>     0.1
> *** Adaptive MCMC:
>     1
> *** Batch size:
>     50
> *** Optimal acceptance ratio:
>     0.44
> *** Name of output directory:
>     ./run.3
> *** Seed for random number generator:
>     192492
> *** CEL files:
>     WTampC_rep1.cel, WTampC_rep2.cel, WTampC_rep3.cel,  
> WTampM_rep1.cel,
> WTampM_rep2.cel, WTampM_rep3.cel
> *** MCMC duration:
>     7h 15m 0s
> Reading mu under condition 1...Read 24707072 items
> Reading mu under condition 2...Read 24707072 items
> Error: cannot allocate vector of size 188.5 Mb
>
>
>
> "If we knew what we were doing, it wouldn't be called Research." -  
> Albert
> Einstein
>
> Louisa Rispoli, Ph.D. Reproductive Physiology
> Department of Animal Science
> University of Tennessee, Knoxville
>
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