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 653
> image(dat.PLM, type="weights", which=6)
> image(dat.PLM, type="resids", which=6)
Furthermore, a Relative Log Expression (RLE) plot can be constructed
from the PLM model. Fo r each array, the RLE plot is a box plot of the
relative ex pression for each gene, which is defined a s the differ ence of the
PLM es timated gene expression and the median expression a c ross arrays.
Yet another useful plot is the Normalized Unscaled Standard Error (NUSE)
plot. The standard error from the PLM fit for each gene on each array is
divided by the median standard error for that gene across all arr ays. The
NUSE plot is a box plot of this normalized
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