AffyPLM's MAplot and cex
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Timothy Wu ▴ 120
@timothy-wu-3964
Last seen 10.3 years ago
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]]
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Ben Bolstad ★ 1.2k
@ben-bolstad-1494
Last seen 7.3 years ago
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
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