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MA Plot
Within computational biology, an MA plot is an application of a Bland–Altman plot for visual representation of genomic data. The plot visualizes the differences between measurements taken in two samples, by transforming the data onto M (log ratio) and A (mean average) scales, then plotting these values. Though originally applied in the context of two channel DNA microarray gene expression data, MA plots are also used to visualise high-throughput sequencing analysis. Explanation Microarray data is often normalized within arrays to control for systematic biases in dye coupling and hybridization efficiencies, as well as other technical biases in the DNA probes and the print tip used to spot the array. By minimizing these systematic variations, true biological differences can be found. To determine whether normalization is needed, one can plot Cy5 (R) intensities against Cy3 (G) intensities and see whether the slope of the line is around 1. An improved method, which is basically a sca ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Biology
Computational biology refers to the use of data analysis, mathematical modeling and computational simulations to understand biological systems and relationships. An intersection of computer science, biology, and big data, the field also has foundations in applied mathematics, chemistry, and genetics. It differs from biological computing, a subfield of computer engineering which uses bioengineering to build computers. History Bioinformatics, the analysis of informatics processes in biological systems, began in the early 1970s. At this time, research in artificial intelligence was using network models of the human brain in order to generate new algorithms. This use of biological data pushed biological researchers to use computers to evaluate and compare large data sets in their own field. By 1982, researchers shared information via punch cards. The amount of data grew exponentially by the end of the 1980s, requiring new computational methods for quickly interpreting ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Frequency Distribution
In statistics, the frequency (or absolute frequency) of an event i is the number n_i of times the observation has occurred/recorded in an experiment or study. These frequencies are often depicted graphically or in tabular form. Types The cumulative frequency is the total of the absolute frequencies of all events at or below a certain point in an ordered list of events. The (or empirical probability) of an event is the absolute frequency normalized by the total number of events: : f_i = \frac = \frac. The values of f_i for all events i can be plotted to produce a frequency distribution. In the case when n_i = 0 for certain i, pseudocounts can be added. Depicting frequency distributions A frequency distribution shows us a summarized grouping of data divided into mutually exclusive classes and the number of occurrences in a class. It is a way of showing unorganized data notably to show results of an election, income of people for a certain region, sales of a product within ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gene Expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, protein or non-coding RNA, and ultimately affect a phenotype, as the final effect. These products are often proteins, but in non-protein-coding genes such as transfer RNA (tRNA) and small nuclear RNA (snRNA), the product is a functional non-coding RNA. Gene expression is summarized in the central dogma of molecular biology first formulated by Francis Crick in 1958, further developed in his 1970 article, and expanded by the subsequent discoveries of reverse transcription and RNA replication. The process of gene expression is used by all known life—eukaryotes (including multicellular organisms), prokaryotes (bacteria and archaea), and utilized by viruses—to generate the macromolecular machinery for life. In genetics, gene expression is the most fundamental level at which the genotype gives rise to the phenotype, '' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RA Plot
The ratio average (RA) plot is an integer-based version of an MA plot for visualizing two-condition count data. Its distinctive arrow-like shape derives from the way it includes condition-unique (0,''n'') or (''n'',0) points into the plot via an epsilon factor. Definition An RA plot, like its cousin, the MA plot, is ''a'' re-scaled and (45-degree) rotated version of ''a'' simple two-dimensional scatter plot of ''a'' versus ''b'' where ''a'' and ''b'' are equal-length vectors of positive measurements. This rescaling and rotation allows for better visibility and emphasis of important outliers points that vary between the two measurement conditions. Essentially it is a plot of the log ratio vs the average log of each pairing of the elements of ''a'' and ''b''. Unlike an MA plot, however, because the RA plot takes non-negative integer counts as input, it must employ work-arounds to include mathematically invisible points (such as points where one or both element(s) of the p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
R (programming Language)
R is a programming language for statistical computing and graphics supported by the R Core Team and the R Foundation for Statistical Computing. Created by statisticians Ross Ihaka and Robert Gentleman, R is used among data miners, bioinformaticians and statisticians for data analysis and developing statistical software. Users have created packages to augment the functions of the R language. According to user surveys and studies of scholarly literature databases, R is one of the most commonly used programming languages used in data mining. R ranks 12th in the TIOBE index, a measure of programming language popularity, in which the language peaked in 8th place in August 2020. The official R software environment is an open-source free software environment within the GNU package, available under the GNU General Public License. It is written primarily in C, Fortran, and R itself (partially self-hosting). Precompiled executables are provided for various operating systems. R ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioconductor
Bioconductor is a Free software, free, Open-source software, open source and Open source software development, open development software project for the analysis and comprehension of Genome, genomic data generated by Wet laboratory, wet lab experiments in molecular biology. Bioconductor is based primarily on the statistics, statistical R (programming language), R programming language, but does contain contributions in other programming languages. It has two Software release life cycle, releases each year that follow the semiannual releases of R. At any one time there is a Software versioning, release version, which corresponds to the released version of R, and a Software versioning, development version, which corresponds to the development version of R. Most users will find the release version appropriate for their needs. In addition there are many genome annotation packages available that are mainly, but not solely, oriented towards different types of microarrays. While computati ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
LOESS
Loess (, ; from german: Löss ) is a clastic, predominantly silt-sized sediment that is formed by the accumulation of wind-blown dust. Ten percent of Earth's land area is covered by loess or similar deposits. Loess is a periglacial or aeolian (windborne) sediment, defined as an accumulation of 20% or less of clay and a balance of roughly equal parts sand and silt (with a typical grain size from 20 to 50 micrometers), often loosely cemented by calcium carbonate. It is usually homogeneous and highly porous and is traversed by vertical capillaries that permit the sediment to fracture and form vertical bluffs. Properties Loess is homogeneous, porous, friable, pale yellow or buff, slightly coherent, typically non- stratified and often calcareous. Loess grains are angular, with little polishing or rounding, and composed of crystals of quartz, feldspar, mica and other minerals. Loess can be described as a rich, dust-like soil. Loess deposits may become very thick, more than ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Normalization (statistics)
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. In another usage in statistics, normalization refers to the creation of shifted and scaled versions of statistics, where the intention is that these normalized values allow the comparison of corresponding normalized values for different datasets i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Binary Logarithm
In mathematics, the binary logarithm () is the power to which the number must be raised to obtain the value . That is, for any real number , :x=\log_2 n \quad\Longleftrightarrow\quad 2^x=n. For example, the binary logarithm of is , the binary logarithm of is , the binary logarithm of is , and the binary logarithm of is . The binary logarithm is the logarithm to the base and is the inverse function of the power of two function. As well as , an alternative notation for the binary logarithm is (the notation preferred by ISO 31-11 and ISO 80000-2). Historically, the first application of binary logarithms was in music theory, by Leonhard Euler: the binary logarithm of a frequency ratio of two musical tones gives the number of octaves by which the tones differ. Binary logarithms can be used to calculate the length of the representation of a number in the binary numeral system, or the number of bits needed to encode a message in information theory. In computer ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bland–Altman Plot
A Bland–Altman plot (difference plot) in analytical chemistry or biomedicine is a method of data plotting used in analyzing the agreement between two different assays. It is identical to a Tukey mean-difference plot, the name by which it is known in other fields, but was popularised in medical statistics by J. Martin Bland and Douglas G. Altman. Agreement versus correlation Bland and Altman drive the point that any two methods that are designed to measure the same parameter (or property) should have good correlation when a set of samples are chosen such that the property to be determined varies considerably. A high correlation for any two methods designed to measure the same property could thus in itself just be a sign that one has chosen a widespread sample. A high correlation does not necessarily imply that there is good agreement between the two methods. Construction Consider a sample consisting of n observations (for example, objects of unknown volume). Both assay ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cyanine
Cyanines, also referred to as tetramethylindo(di)-carbocyanines are a synthetic dye family belonging to the polymethine group. Although the name derives etymologically from terms for shades of blue, the cyanine family covers the electromagnetic spectrum from near IR to UV. Chemically, cyanines are a conjugated system between two nitrogen atoms; in each resonance structure, exactly one nitrogen atom is oxidized to an iminium. Typically, they form part of a nitrogenous heterocyclic system. The main application for cyanine dyes is in biological labeling. Nevertheless, there is a wide literature on both their synthesis and uses, and cyanines are common in some CD and DVD media. Structure Cyanines have been classified in many ways: * ''Streptocyanines'' or ''open chain cyanines'': : R2N+=CH H=CH'n''-NR2 (I) * ''Hemicyanines'': : Aryl=N+=CH H=CH'n''-NR2 (II) * ''Closed chain cyanines'': :Aryl=N+=CH H=CH'n''-N=Aryl (III) Additionally, these classes are recognized: * ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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