Problems with the size of the plots obtained with AffyPLM
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@jordi-altirriba-gutierrez-682
Last seen 5.7 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 _________________________________________________________________ Grandes ?xitos, superh?roes, imitaciones, cine y TV...
cdf affy gcrma affyPLM affyio cdf affy gcrma affyPLM affyio • 1.6k views
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@oosting-j-path-412
Last seen 10.2 years ago
You could save the Pset object to a file and load it in at your Windows computer to create the images. At that time the linear model has been fitted, and the amount of needed memory should be a lot less. Jan -----Original Message----- 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).
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Dear Jan Many thanks for your answer, but I can?t open a session in Windows which has been created with Linux. What I do is: At the end of my Lynux session: >save.image(?test.RData?) I export this file to the Windows PC and execute: >load(?test.RData?) Error in load(?test.RData?) ReadItem: type 25 unknown (I have translated it from the Spanish). Nevertheless, many thanks, Jordi >From: <j.oosting at="" lumc.nl=""> >To: <altirriba at="" hotmail.com="">,<bioconductor at="" stat.math.ethz.ch=""> >Subject: RE: [BioC] Problems with the size of the plots obtained with >AffyPLM >Date: Wed, 17 Jan 2007 09:28:15 +0100 > >You could save the Pset object to a file and load it in at your Windows >computer to create the images. At that time the linear model has been >fitted, and the amount of needed memory should be a lot less. > >Jan > >-----Original Message----- > 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). > _________________________________________________________________ ?Est?s pensando en cambiar de coche? Todas los modelos de serie y extras en
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It should not be a problem to load in data on windows when it is saved in linux if the version of R is the same on both sides. You could try to save just the Pset object by save(Pset,file="test.RData",compress=FALSE) Be sure to load the affyPLM library before loading in the file Jan -----Original Message----- From: Jordi Altirriba Guti?rrez [mailto:altirriba@hotmail.com] Sent: woensdag 17 januari 2007 16:27 To: Oosting, J. (PATH); bioconductor at stat.math.ethz.ch Subject: RE: [BioC] Problems with the size of the plots obtained with AffyPLM Dear Jan Many thanks for your answer, but I can't open a session in Windows which has been created with Linux. What I do is: At the end of my Lynux session: >save.image("test.RData") I export this file to the Windows PC and execute: >load("test.RData") Error in load("test.RData") ReadItem: type 25 unknown (I have translated it from the Spanish). Nevertheless, many thanks, Jordi >From: <j.oosting at="" lumc.nl=""> >To: <altirriba at="" hotmail.com="">,<bioconductor at="" stat.math.ethz.ch=""> >Subject: RE: [BioC] Problems with the size of the plots obtained with >AffyPLM >Date: Wed, 17 Jan 2007 09:28:15 +0100 > >You could save the Pset object to a file and load it in at your Windows >computer to create the images. At that time the linear model has been >fitted, and the amount of needed memory should be a lot less. > >Jan > >-----Original Message----- > 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). > _________________________________________________________________ ?Est?s pensando en cambiar de coche? Todas los modelos de serie y extras en MSN Motor. http://motor.msn.es/researchcentre/
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Dear Jan Many thanks for your answer!! (sorry for the delay, too much work in the lab...) The R version was different between the 2 computers. Now I have installed the same version in the Windows machine and I have done the jpeg image without any problem, scaled correctly and with a reasonable size. Again, many thanks!! Yours sincerelly, Jordi >From: <j.oosting at="" lumc.nl=""> >To: <altirriba at="" hotmail.com=""> >CC: <bioconductor at="" stat.math.ethz.ch=""> >Subject: RE: [BioC] Problems with the size of the plots obtained with >AffyPLM >Date: Wed, 17 Jan 2007 17:06:08 +0100 > >It should not be a problem to load in data on windows when it is saved in >linux if the version of R is the same on both sides. >You could try to save just the Pset object by >save(Pset,file="test.RData",compress=FALSE) >Be sure to load the affyPLM library before loading in the file > >Jan > >-----Original Message----- >From: Jordi Altirriba Guti?rrez [mailto:altirriba at hotmail.com] >Sent: woensdag 17 januari 2007 16:27 >To: Oosting, J. (PATH); bioconductor at stat.math.ethz.ch >Subject: RE: [BioC] Problems with the size of the plots obtained with >AffyPLM > >Dear Jan >Many thanks for your answer, but I can't open a session in Windows which >has been created with Linux. > >What I do is: >At the end of my Lynux session: > >save.image("test.RData") >I export this file to the Windows PC and execute: > >load("test.RData") >Error in load("test.RData") >ReadItem: type 25 unknown (I have translated it from the Spanish). > >Nevertheless, many thanks, > >Jordi > > > >From: <j.oosting at="" lumc.nl=""> > >To: <altirriba at="" hotmail.com="">,<bioconductor at="" stat.math.ethz.ch=""> > >Subject: RE: [BioC] Problems with the size of the plots obtained with > >AffyPLM > >Date: Wed, 17 Jan 2007 09:28:15 +0100 > > > >You could save the Pset object to a file and load it in at your Windows > >computer to create the images. At that time the linear model has been > >fitted, and the amount of needed memory should be a lot less. > > > >Jan > > > >-----Original Message----- > > 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). > > > >_________________________________________________________________ >?Est?s pensando en cambiar de coche? Todas los modelos de serie y extras en >MSN Motor. http://motor.msn.es/researchcentre/ > _________________________________________________________________ Moda para esta temporada. Ponte al d?a de todas las tendencias.
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