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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.
This will allow you to type text that you want to add, using wiki markup to format the text and to add other elements like images and tables that are explained later in this tutorial. Wiki markup can initially seem intimidating (especially references) but it actually requires only a few rules to understand and use.
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]
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.
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The p-value for the permutation test is the proportion of the r values generated in step (2) that are larger than the Pearson correlation coefficient that was calculated from the original data. Here "larger" can mean either that the value is larger in magnitude, or larger in signed value, depending on whether a two-sided or one-sided test is ...
A parity plot is a scatterplot that compares a set of results from a computational model against benchmark data. Each point has coordinates ( x , y ), where x is a benchmark value and y is the corresponding value from the model.