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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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 sc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Epsilon
Epsilon (, ; uppercase , lowercase or lunate ; el, έψιλον) is the fifth letter of the Greek alphabet, corresponding phonetically to a mid front unrounded vowel or . In the system of Greek numerals it also has the value five. It was derived from the Phoenician letter He . Letters that arose from epsilon include the Roman E, Ë and Ɛ, and Cyrillic Е, È, Ё, Є and Э. The name of the letter was originally (), but it was later changed to ( 'simple e') in the Middle Ages to distinguish the letter from the digraph , a former diphthong that had come to be pronounced the same as epsilon. The uppercase form of epsilon is identical to Latin E but has its own code point in Unicode: . The lowercase version has two typographical variants, both inherited from medieval Greek handwriting. One, the most common in modern typography and inherited from medieval minuscule, looks like a reversed number "3" and is encoded . The other, also known as lunate or uncial epsilon ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sandrine Dudoit
Sandrine Dudoit is a professor of statistics and public health at the University of California, Berkeley. Her research applies statistics to microarray and genetic data; she is known as one of the founders of the open-source Bioconductor project for the development of bioinformatics software. Education and career Dudoit studied for the French baccalauréat in mathematics and physical sciences at the in Paris. She moved to Canada for her undergraduate studies, completing a bachelor's degree in mathematics in 1992 at Carleton University. As a beginning graduate student in the department of statistics at the University of California, Berkeley, Dudoit was the recipient of the Gertrude Cox Scholarship of the American Statistical Association's Committee on Women in Statistics. She earned her doctorate at Berkeley in 1999. Her dissertation, ''Linkage Analysis of Complex Human Traits Using Identity by Descent Data'', was supervised by Terry Speed. Career and research After postdoctoral r ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Jean Yang
Jean Yee Hwa Yang is an Australian statistician known for her work on variance reduction for microarrays, and for inferring proteins from mass spectrometry data. Yang is a Professor in the School of Mathematics and Statistics at the University of Sydney. Education and career Yang studied at Killara High School between 1987 and 1990 and at Barker College between 1991 and 1992. She earned a bachelor's degree with first class honours and a University Medal from the University of Sydney in 1996, in mathematics and statistics. After working for half a year at the Commonwealth Scientific and Industrial Research Organisation, Yang then went to the University of California, Berkeley, for graduate study, completing her Ph.D. in statistics in 2002. Her dissertation, "Statistical methods in the design and analysis of gene expression data from cDNA microarray experiment", was supervised by Terry Speed. Yang did postdoctoral research in biostatistics and bioinformatics with Mark R. Segal at ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Terry Speed
Terence Paul "Terry" Speed (born 14 March 1943 in Victor Harbor, South Australia), FAA FRS is an Australian statistician. A senior principal research scientist at the Walter and Eliza Hall Institute of Medical Research, he is known for his contributions to the analysis of variance and bioinformatics, and in particular to the analysis of microarray data. Early life and education Terry Speed was born in Victor Harbor, in South Australia, and grew up in Melbourne. In 1961, he started a joint degree in medicine and science at the University of Melbourne, but later focussed on science only, obtaining a honours degree in mathematics and statistics in 1964. Speed obtained a Ph.D. from Monash University in 1968 with a thesis titled ''Some topics in the theory of distributive lattices'' under the supervision of Peter D. Finch. Career After his PhD, Terry Speed took a lecturing position in Sheffield (United Kingdom), at the Manchester-Sheffield School of Probability and Statistics. I ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Line (geometry)
In geometry, a line is an infinitely long object with no width, depth, or curvature. Thus, lines are one-dimensional objects, though they may exist in two, three, or higher dimension spaces. The word ''line'' may also refer to a line segment in everyday life, which has two points to denote its ends. Lines can be referred by two points that lay on it (e.g., \overleftrightarrow) or by a single letter (e.g., \ell). Euclid described a line as "breadthless length" which "lies evenly with respect to the points on itself"; he introduced several postulates as basic unprovable properties from which he constructed all of geometry, which is now called Euclidean geometry to avoid confusion with other geometries which have been introduced since the end of the 19th century (such as non-Euclidean, projective and affine geometry). In modern mathematics, given the multitude of geometries, the concept of a line is closely tied to the way the geometry is described. For instance, in analy ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Vector (geometric)
In mathematics, physics, and engineering, a Euclidean vector or simply a vector (sometimes called a geometric vector or spatial vector) is a geometric object that has magnitude (or length) and direction. Vectors can be added to other vectors according to vector algebra. A Euclidean vector is frequently represented by a ''directed line segment'', or graphically as an arrow connecting an ''initial point'' ''A'' with a ''terminal point'' ''B'', and denoted by \overrightarrow . A vector is what is needed to "carry" the point ''A'' to the point ''B''; the Latin word ''vector'' means "carrier". It was first used by 18th century astronomers investigating planetary revolution around the Sun. The magnitude of the vector is the distance between the two points, and the direction refers to the direction of displacement from ''A'' to ''B''. Many algebraic operations on real numbers such as addition, subtraction, multiplication, and negation have close analogues for vectors, operations ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Jitter
In electronics and telecommunications, jitter is the deviation from true periodicity of a presumably periodic signal, often in relation to a reference clock signal. In clock recovery applications it is called timing jitter. Jitter is a significant, and usually undesired, factor in the design of almost all communications links. Jitter can be quantified in the same terms as all time-varying signals, e.g., root mean square (RMS), or peak-to-peak displacement. Also, like other time-varying signals, jitter can be expressed in terms of spectral density. Jitter period is the interval between two times of maximum effect (or minimum effect) of a signal characteristic that varies regularly with time. Jitter frequency, the more commonly quoted figure, is its inverse. ITU-T G.810 classifies jitter frequencies below 10 Hz as wander and frequencies at or above 10 Hz as jitter. Jitter may be caused by electromagnetic interference and crosstalk with carriers of other signals. Jitte ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DNA Microarray
A DNA microarray (also commonly known as DNA chip or biochip) is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome. Each DNA spot contains picomoles (10−12 moles) of a specific DNA sequence, known as '' probes'' (or ''reporters'' or '' oligos''). These can be a short section of a gene or other DNA element that are used to hybridize a cDNA or cRNA (also called anti-sense RNA) sample (called ''target'') under high-stringency conditions. Probe-target hybridization is usually detected and quantified by detection of fluorophore-, silver-, or chemiluminescence-labeled targets to determine relative abundance of nucleic acid sequences in the target. The original nucleic acid arrays were macro arrays approximately 9 cm × 12 cm and the first computerized image based analysis was published in 1981. It was i ... [...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] |
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 phen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Microarrays
A microarray is a multiplex lab-on-a-chip. Its purpose is to simultaneously detect the expression of thousands of genes from a sample (e.g. from a tissue). It is a two-dimensional array on a solid substrate—usually a glass slide or silicon thin-film cell—that assays (tests) large amounts of biological material using high-throughput screening miniaturized, multiplexed and parallel processing and detection methods. The concept and methodology of microarrays was first introduced and illustrated in antibody microarrays (also referred to as antibody matrix) by Tse Wen Chang in 1983 in a scientific publication and a series of patents. The " gene chip" industry started to grow significantly after the 1995 ''Science Magazine'' article by the Ron Davis and Pat Brown labs at Stanford University. With the establishment of companies, such as Affymetrix, Agilent, Applied Microarrays, Arrayjet, Illumina, and others, the technology of DNA microarrays has become the most sophisticat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
