[BioC] how to reduce the file size of scatter plot matrix

[Michael Seewald]

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.

Dear Caimiao,

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.

Best regards,
Michael