Hi Caimiao yet two more options: - use "png" or "jpeg" as an output device. For these the output file size is limited by the number of pixels in the image. - use Jelle Goeman's and Paul Eilers' fast scatterplot smoother http://www.math.leidenuniv.nl/~jgoeman Best wishes Wolfgang James Wettenhall wrote: > On Mon, 12 Jul 2004, Caimiao Wei wrote: > >>I am trying to get the scatter plot matrix (function "pairs") >>and MVA plot (function "mva.pairs") of multiple affy chips. >>When I use postscript() or pdf() to save the graphs generated >>from 12 affy mouse chips using the "pairs" function, the size >>of the file is about 500 MB. I would appreciate any >>suggestions that can effectively reduces the size of these plots. ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/abt0840/whuber

Hi Michael > I think the png() command is what you should use. Using postscript() or pdf() > will essentially duplicate your data and project it into postscript > expressions. If you are only interested in the picture, png() is the way of > choice. jpeg() is IMHO not a good alternative, as it will smear out hard > contrasts, which are abundant in scientific plots. ... while we're talking about image quality: I often use a sequence of commands like dev.copy(pdf, file="img.pdf", height=..., width=...) dev.off() system("convert -density 360 img.pdf -compress RLE img.tif") file.remove("img.pdf") which assumes that the program "convert" from the imageMagick package is in your path and is of course a little clumsy compared to talking to a real device but works well e.g. for inclusion of images in Powerpoint. Best wishes Wolfgang -- ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/abt0840/whuber