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

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 _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]