hi i generated one graph by using command plotDensities(MA) for agilent two color array.but i could not understand what does mean of Densities using on y axis. Can you help me please to understand the graph,about what exactly on x axis and what is on y axis. thanking you, NEERAJ RANA JRF ,INDIAN INSTITUTE OF SCIENCE(BANGLORE) INDIA. [[alternative HTML version deleted]]

Hello Neeraj: The help command '?plotDensities' provides a description: Plots the densities of individual-channel intensities for two-color microarray data. Internally it uses the density() function to construct an estimate of the probability density function underlying the data. Basically, it displays the distribution of the data, i.e., the densityplot should fall nicely on the histogram of the data. X-axis is the range of the data values (R/G intensities, in this case, Y-axis, the probability). The number of red (or green) lines corresponds to the number of arrays. For example, I reproduce the results from plotDensities() with hist()+density()+plot(). Since I do not have the data you used, I am using some given at the end of the above-mentioned help page. # load data library(sma) library(limma) data(MouseArray) MA.n=MA.RG(mouse.data) # extract # make space for four plots par(mfrow=c(2,2)) # Plot 1: plotDensities() plotDensities(MA.n[,1]) # Plot 2: just plotting the red channel using hist/density/plot Rvals=log2((mouse.data$R-mouse.data$Rb)[,1]) # background subtraction hist(Rvals, prob=T, breaks="scott", border="gray", xlim=c(7,16), main="Red channel", xlab="Log intensity") lines(density(Rvals), col="red", lwd=2) # Plot 3: just plotting the green channel using hist/density/plot Gvals=log2((mouse.data$G-mouse.data$Gb)[,1]) # background subtraction hist(Gvals, prob=T, breaks="scott", border="gray", xlim=c(7,16), main="Green channel", xlab="Log intensity") lines(density(Gvals), col="green", lwd=2) # Plot 4: just plotting the green channel using hist/density/plot plot(density(Rvals), col="red", type="l", lwd=2, main="Both channels", xlab="Log intensity", xlim=c(7,16)) lines(density(Gvals), col="green", lwd=2) [My sessionInfo() at the end of this message] Best, Saroj > sessionInfo() R version 2.9.0 (2009-04-17) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_ MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_A DDRESS=C;L C_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_2.18.2 sma_0.5.15 loaded via a namespace (and not attached): [1] tools_2.9.0 neeraj rana wrote: > hi > > i generated one graph by using command plotDensities(MA) for agilent two > color array.but i could not understand what does mean of Densities using on > y axis. > Can you help me please to understand the graph,about what exactly on x axis > and what is on y axis. > > > thanking you, > NEERAJ RANA > JRF ,INDIAN INSTITUTE OF SCIENCE(BANGLORE) > INDIA. > > [[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 > >