[BioC] BGX Output Help

[Louisa A Rispoli/AS/EXP/UTIA]

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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?

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