[Bioc-devel] strange behavior on memory usage (fwd)

[Benilton Carvalho]

hi everyone,

i was wondering if anybody could give me a hint of what causes a strange 
behavior on memory usage when using oligo/makePlatformDesign packages.

i'm reading a bunch of (affy) SNP chips:

> x = read.celfiles(list.celfiles())
     -> at this point the R process uses around 2GB
     -> which does not look bad, since i'm reading 90 samples
> show(x)
     -> now the R process uses around 6GB
     -> how can i improve the code so it does not uses so much memory?
     -> the information i'm using at this step comes basically from
     ->       dim(getExpData(x, "exprs"))
> gc()
     -> back to 2GB

in the above, 'x' is an oligoBatch object (which contains eSet, details at the 
end of this message).

any suggestion?

thanks a lot,

benilton

ps: i just noticed that using dim(exprs(x)) in show() reduces the memory usage 
from 6GB to 3.5GB... and using str(x) increases it to 10.5GB.

-----------------------------------------------------------------------------
R version 2.2.0, 2005-07-26, x86_64-unknown-linux-gnu

attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "base"

other attached packages:
      oligo reposTools    Biobase
    "0.0.7"    "1.6.0"    "1.6.6"
-------------------------------------------------------------------------------

> str(x)
Formal class 'oligoBatch' [package "oligo"] with 8 slots
   ..@ manufacturer: chr "Affymetrix"
   ..@ platform    : chr "Mapping50K_Hind240"
   ..@ eList       :Formal class 'exprList' [package "Biobase"] with 2 slots
   .. .. ..@ eMetadata:`data.frame':     0 obs. of  0 variables
   .. .. ..@ eList    :List of 1
   .. .. .. ..$ exprs: num [1:2560000, 1:90]  1369 65472  ...
   .. .. .. .. ..- attr(*, "dimnames")=List of 2
   .. .. .. .. .. ..$ : NULL
   .. .. .. .. .. ..$ : chr [1:90] "NA06985_Hind_B5_3005533.CEL" ...
   ..@ description :Formal class 'MIAME' [package "Biobase"] with 11 slots
   .. .. ..@ name          : chr ""
   .. .. ..@ lab           : chr ""
   .. .. ..@ contact       : chr ""
   .. .. ..@ title         : chr ""
   .. .. ..@ abstract      : chr ""
   .. .. ..@ url           : chr ""
   .. .. ..@ samples       : list()
   .. .. ..@ hybridizations: list()
   .. .. ..@ normControls  : list()
   .. .. ..@ preprocessing :List of 2
   .. .. .. ..$ filenames   : chr [1:90] "NA06985_Hind_B5_3005533.CEL" ...
   .. .. .. ..$ oligoversion: chr NA
   .. .. ..@ other         : list()
   ..@ annotation  : chr ""
   ..@ sampleNames : chr [1:90] "NA06985_Hind_B5_3005533.CEL" ...
   ..@ notes       : chr ""
   ..@ phenoData   :Formal class 'phenoData' [package "Biobase"] with 3 slots
   .. .. ..@ pData      :`data.frame':   90 obs. of  1 variable:
   .. .. .. ..$ sample: int [1:90] 1 2 3 4 5 6 7 8 9 10 ...
   .. .. ..@ varLabels  :List of 1
   .. .. .. ..$ sample: chr "arbitrary numbering"
   .. .. ..@ varMetadata:`data.frame':   0 obs. of  0 variables