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Jordi Altirriba Gutiérrez ▴ 350@jordi-altirriba-gutierrez-682
Last seen 3.5 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:  "splines" "tools" "methods" "stats" "graphics" "grDevices"  "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 _________________________________________________________________ Grandes ?xitos, superh?roes, imitaciones, cine y TV...