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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716 Statistics and Data Analysis for Microarrays Using R and Bioconductor
20.4.2 Signal calculation
As for cDNA arrays, the goal of the preprocessing is to modify the gene-
specific intensity values in order to obta in a value that reflects as accurately
as p ossible the amount of transcript in the solution used. As noted before,
Affymetrix arrays use several probes with both pe rfect matches (PM) and
mismatched (MM) cells. The challenge is to combine these values in a unique,
meaningful value, proportional to the transcript. The amount of hybridization
on the mismatched sequence is thought to be representative for nonspecific hy-
bridization, and its
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