Hello, Caveat, I'm pretty new to R. I'm trying AffyPLM's MAplot by following example from "Quality Assessment of Affymetrix GeneChip Data" by Bolstad, et al. ( http://www.springerlink.com/content/x88745lrpk331352/?p=5fe62472106447 78b597610f5a5c6b43&pi=2) On page 36 when I made a call to MAplot(data, cex = 0.75). I tried changing the cex parameter to a small value (0.1), it appeared that not only text are made smaller, plots were also made smaller without corresponding change in coordinates. What I mean is a dot on a MA plot is changed in position in respect to the coordinates. This was not what I was expecting. My intention is only to change the size of the text "Median", "IQR" as well as the title. Was this normal? Timothy [[alternative HTML version deleted]]

By setting the cex so small you have essentially thinned the number of points that you are going to see. You could see the same effect x <- rnorm(100000) y <- rnorm(100000) plot(x,y,pch=".") plot(x,y,pch=".",cex=0.1) Why that happens is not really specific to the MAplot() command. Now you could also try something like MAplot(Data,cex=0.1,pch=20) which may or may not acheive the effect you desired. Ypu can also use cex.main to control the size of the title. eg MAplot(Data,cex.main=0.1) On Wed, 2010-03-17 at 13:52 +0800, Timothy Wu wrote: > Hello, > > Caveat, I'm pretty new to R. > > I'm trying AffyPLM's MAplot by following example from "Quality Assessment of > Affymetrix GeneChip Data" by Bolstad, et al. ( > http://www.springerlink.com/content/x88745lrpk331352/?p=5fe624721064 4778b597610f5a5c6b43&pi=2) > > On page 36 when I made a call to MAplot(data, cex = 0.75). I tried changing > the cex parameter to a small value (0.1), it appeared that not only text are > made smaller, plots were also made smaller without corresponding change in > coordinates. What I mean is a dot on a MA plot is changed in position in > respect to the coordinates. This was not what I was expecting. My intention > is only to change the size of the text "Median", "IQR" as well as the title. > > Was this normal? > > Timothy > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor