[BioC] what does mean of Densities on y axis in the graph generated by plotDensities

[Saroj K Mohapatra]

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_ADDRESS=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.
>
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>
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