[BioC] Problems with the size of the plots obtained with AffyPLM

[Jordi Altirriba Gutiérrez]

  Dear BioC users,
  I am assessing the quality of 20 Affymetrix arrayx of the type 
HGU-133-Plus-2 through the AffyPLM package.
  Due to memory problems, I am using a remote PC with 2Gb of RAM with a 
Linux OS (I have very little experience using X OS).
  Everything is OK, but I can’t plot the image obtained with AffyPLM with 
this command:
 > image(Pset,which=1)
  The fact of using a remote connection, forces the use of postscript as the 
only way to obtain an image (I can’t open the X11 device with others 
commands as jpeg).

  I obtain these errors

A) Problems with the margins:
>postscript("QC.ps")
>par(mfrow=c(7,3))
>image(Pset,which=1)
Error in plot.new() : figure margins too large

B) Problems with the file size:
>postscript("QC.ps")
>par(mfrow=c(7,3), mar=rep(1, 4))
>image(Pset,which=1)


>image(Pset,which=20)
>dev.off()

The file obtained has a size of 805Mb, which is too big to work with it.

I have tried to modify the values of mar (mar=c(0.1,0.1,0.1,0.1)) and the 
file have the same size. Moreover, I have tried to modify the postscript 
size postscript("QC.ps", width=1, height=1), without success.

Is any way to solve this problem? (Probably there is a really easy way which 
due to my inexperience I can’t found, sorry. I have been googling without 
success). In other studies, using jpeg command and a Windows OS, the images 
produced have a reasonable size and the images are scaled to the dimensions 
of the plot.

My session info:
>sessionInfo()
R version 2.4.0 (2006-10-03)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=en_US;LC_
MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREME
NT=en_US;LC_IDENTIFICATION=C

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

other attached packages:
hgu133plus2cdf        affyPLM          gcrma    matchprobes       affydata
      "1.14.0"       "1.10.0"        "2.6.0"        "1.6.0"       "1.10.0"
          affy         affyio        Biobase
      "1.12.1"        "1.2.0"       "1.12.2"

Many thanks for your advices,

Yours faithfully,

Jordi Altirriba
PhD student
Barcelona, Spain

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