Download e-book for iPad: Advanced analysis of gene expression microarray data by Aidong Zhang

By Aidong Zhang

ISBN-10: 9812566457

ISBN-13: 9789812566454

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

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4) Repeat the steps above until the changes between consecutive steps are below a given threshold. (5) Normalize xii using the regression line found above: (x2i)n = x2i -m+b. 1 Intensity-Dependent Normalization LOWESS: Locally weighted linear regression Several reports have indicated that the log2(ratio) values can have a systematic dependence on the intensity [315,317]. This most commonly appears as a deviation from zero for low-intensity spots. Locally weighted linear regression (LOWESS) [58] analysis has been proposed [315,317] as a normalization method that can remove such intensity-dependent effects in the log2{ratio) values.

Among other sources of variability, systematic bias can be caused by the concentration and amount of DNA placed on the microarrays, wear to arraying equipment such as spotting pins, the quantities of mRNA extracted from samples, reverse transcription bias, lack of spatial homogeneity of the slides, scanner settings, saturation effects, background fluorescence, linearity of detection response, and ambient conditions [10]. 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].

Such redundancy is actually a valuable feature of the genetic code, rendering it more robust in the event of small errors in the transcription process. This will be discussed in the next subsection. 2 Transcription and Gene Expression Transcription is the process of synthesizing R N A using genes as templates. A gene is expressed when, t h r o u g h the transcription process, its coding is transferred to an R N A molecule. To initiate a transcription process, the DNA double helix is "unzipped," starting at the promoter site of a gene.

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Advanced analysis of gene expression microarray data by Aidong Zhang

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