Advanced analysis of gene expression microarray data by Aidong Zhang

By Aidong Zhang

This booklet is especially good written, in nice aspect and readability. The name "Advanced" sounds formidable to a few intermediate or access point statisticians, however the math information within the publication is especially comprehensible, provided as important aid as a way to comprehend the defined statistical tools.
I may hugely suggest this e-book to statisticians with all statistical backgrounds who're new to the realm of microarray info research. This booklet is ideal as a textbook for a primary process microarray info research too.

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4, we will then describe the steps involved in a microarray experiment. The raw data resulting from a microarray experiment may contain noise, missing values, and experimental bias. Therefore pre-processing and normalization of the raw data is indispensable before any further analysis can be performed. 6, respectively. 2 Microarray Chip Manufacture There are two main approaches to manufacture of microarray chips: deposition of DNA fragments by robotic spotting and in situ synthesis [173]. Manufacture by robotic deposition may proceed through the deposition of PCR-amplified cDNA clones or the printing of already-synthesized oligonucleotides.

In addition, dye bias is present in almost all multichannel experiments. Generally, Cy5 (red) intensities tend to be higher than Cy3 (green) intensities, but the magnitude of the difference generally depends on the overall intensity [10]. The reasons for the imbalance between the channels are as follows [266]: • The Cy3 and Cy5 labels may be differentially incorporated into DNA samples with varying frequencies of occurrence. • The Cy3 and Cy5 dyes may have different emission responses to the excitation laser at different frequencies of occurrence.

This technique employs (radioactively) labeled DNA (or RNA) probes to hybridize to identify very similar DNA sequences placed on a nitrocellulose filter called a blot. The number of DNA bands t h a t hybridize to a short probe gives an estimate of the number of closely related genes in an organism [299]. Similar techniques are the Northern blot and the Western blot, which, respectively, employ RNA strands and proteins in lieu of DNA sequences. T h e basic principle behind these techniques is t h a t DNA and RNA strands can be labeled for detection and then used to probe other nucleic acid molecules t h a t have been attached to a solid surface.

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