Oligo plots use a random sample of the data to produce the plots. Check the
"nsample" argument. b

On 20 Apr 2011 08:06, "Javier Pérez Florido" <jpflorido@gmail.com> wrote:

Dear list,
I'm checking the quality of a set of raw Human Gene ST 1.0 arrays through
the use of boxplots and histograms. CEL files are read using read.celfiles
from oligo package.
Then, boxplots and histograms are plot using "boxplot" and "hist" commands
respectively, but I observe some differences between the plots given by
these commands and the plots of "manual" boxplots and histograms such these:

pms = log2(pm(OligoRaw))
dens = oligo:::matDensity(pms)
cols = darkColors(ncol(pms))
boxplot(as.data.frame(pms), range=0, col=cols)
matplot(dens[["x"]], dens[["y"]], type="l", lwd=2,
col=cols,xlab="log-intensity", ylab="density")

where "OligoRaw" is the object that holds raw data from the CEL files.
To be more precise, in boxplots there are differences in the values related
to Q3+1.5*IQR. In the "manual" boxplot, these values are bigger than in the
standard boxplot command.
On the other hand, in histograms, the differences are related to the CEL
files with the biggest density values. In the "manual" histogram (matplot),
these values are bigger than in the standard hist command.

Why do these differences exist?
Thanks,
Javier

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