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knitr is a software engine for dynamic report generation with R. [1] [2] It is a package in the programming language R that enables integration of R code into LaTeX, LyX, HTML, Markdown, AsciiDoc, and reStructuredText documents. The purpose of knitr is to allow reproducible research in R through the means of literate programming.
A mathematical markup language is a computer notation for representing mathematical formulae, based on mathematical notation.Specialized markup languages are necessary because computers normally deal with linear text and more limited character sets (although increasing support for Unicode is obsoleting very simple uses).
A common method for evaluating how well normalized an array is, is to plot an MA plot of the data. MA plots can be produced using programs and languages such as R and MATLAB. [6] [7] Raw Affy data contains about twenty probes for the same RNA target. Half of these are "mismatch spots", which do not precisely match the target sequence.
MATLAB (an abbreviation of "MATrix LABoratory" [18]) is a proprietary multi-paradigm programming language and numeric computing environment developed by MathWorks.MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages.
Examples of domain-specific programming languages include HTML, Logo for pencil-like drawing, Verilog and VHDL hardware description languages, MATLAB and GNU Octave for matrix programming, Mathematica, Maple and Maxima for symbolic mathematics, Specification and Description Language for reactive and distributed systems, spreadsheet formulas and ...
Markdown [9] is a lightweight markup language for creating formatted text using a plain-text editor. John Gruber created Markdown in 2004 as an easy-to-read markup language. [9] Markdown is widely used for blogging and instant messaging, and also used elsewhere in online forums, collaborative software, documentation pages, and readme files.
Area-based counts often utilize quadrants, which are sampling areas or volumes of any size or shape. For example, a quadrat could be a 0.25 × 0.25-meter square plot for counting small plants, a 0.1-hectare plot for counting trees, or a soil core of a certain diameter and depth for counting soil organisms.
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 scaled, 45 degree rotation of the R vs. G plot is an MA-plot. [4]