April 2016
Beginner to intermediate
1036 pages
33h 39m
English
book
Statistics and Data Analysis for Microarrays Using R and Bioconductor, 2nd Edition
by Sorin Draghici
Content preview from Statistics and Data Analysis for Microarrays Using R and Bioconductor, 2nd Edition
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Quality control 663
> plotMAXY(sumraw, arrays=1:ncol(sumraw), pch=16)
Array probe intensity distr ibution can be plotted as follows:
> plot(density(log2(sumraw[,1]),na.rm=TRUE), col=usr.col[1],
+ xlab="log2(intensity)", main=NA)
> for (i in 2:ncol(sumraw)) {
+ lines(density(log2(sumraw[,i]),na.rm=TRUE), col=usr.col[i])
+ }
> legend("topright",colnames(sumraw), lty=1, col=usr.col)
19.3.2.2 Raw probe data import, visualization, and quality assess-
ment using “lumi”
There is an alternative package “lumi”[135] that includes functions designed
for preprocessing bead-summary level data. This package offers e ven more
visualization and assessment methods. Here, we brie fly outline some basic
functions available for step-wise preproces sing. A wrapper function
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