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Normalization

In statistics and applications of statistics, normalization can have a range of meanings. In the simplest cases, normalization of ratings means adjusting values measured on different scales to a notionally common scale, often prior to averaging. In more complicated cases, normalization may refer to more sophisticated adjustments where the intention is to bring the entire probability distributions of adjusted values into alignment. In the case of normalization of scores in educational assessment, there may be an intention to align distributions to a normal distribution. A different approach to normalization of probability distributions is quantile normalization, where the quantiles of the different measures are brought into alignment. [Source: Wikipedia]

HCS-Analyzer

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

High-throughput screening is a powerful technology principally used by pharmaceutical industries allowing the identification of molecules of interest within large libraries. Originally target based, cellular assays provide a way to test compounds (or other biological material such as small interfering RNA) in a more physiologically realistic in vitro environment. High-content screening (HCS) platforms are now available at lower cost, giving the opportunity for universities or research institutes to access those technologies for research purposes.

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A personalized microRNA microarray normalization method using a logistic regression model

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNA (miRNA) is a set of newly discovered non-coding small RNA molecules. Its significant effects have contributed to a number of critical biological events including cell proliferation, apoptosis development, as well as tumorigenesis. High-dimensional genomic discovery platforms (e.g. microarray) have been employed to evaluate the important roles of miRNAs by analyzing their expression profiling.

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BeadSme

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

Compared with complementary DNA (cDNA) or messenger RNA (mRNA) microarray data, microRNA (miRNA) microarray data are harder to normalize due to the facts that the total number of miRNAs is small, and that the majority of miRNAs usually have low expression levels. In bead-based microarrays, the hybridization is completed in several pools. As a result, the number of miRNAs tested in each pool is even smaller, which poses extra difficulty to intrasample normalization and ultimately affects the quality of the final profiles assembled from various pools.

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MmPalateMiRNA

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

MicroRNAs (miRNAs) constitute the largest family of noncoding RNAs involved in gene silencing and represent critical regulators of cell and tissue differentiation. Microarray expression profiling of miRNAs is an effective means of acquiring genome-level information of miRNA activation and inhibition, as well as the potential regulatory role that these genes play within a biological system.

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ExiMiR

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

High-quality expression data are required to investigate the biological effects of microRNAs (miRNAs). The goal of this study was, first, to assess the quality of miRNA expression data based on microarray technologies and, second, to consolidate it by applying a novel normalization method. Indeed, because of significant differences in platform designs, miRNA raw data cannot be normalized blindly with standard methods developed for gene expression.

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NanoStringNorm

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

The NanoString nCounter Platform is a new and promising technology for measuring nucleic acid abundances. It has several advantages over PCR-based techniques, including avoidance of amplification, direct sequence interrogation and digital detection for absolute quantification. These features minimize aspects of experimental error and hold promise for dealing with challenging experimental conditions such as archival formalin-fixed paraffin-embedded samples.

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NqA

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

In this note, we propose an R function named NqA (Normalization qPCR Array, where qPCR is quantitative real-time polymerase chain reaction) suitable for the identification of a set of microRNAs (miRNAs) to be used for data normalization in view of subsequent validation studies with qPCR data.

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