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Jordi Altirriba Gutiérrez
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350
@jordi-altirriba-gutierrez-682
Last seen 5.6 years ago
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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