smile.data.parser.microarray.package-info Maven / Gradle / Ivy
/*******************************************************************************
* Copyright (c) 2010 Haifeng Li
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*******************************************************************************/
/**
* Parsers for microarray gene expression datasets. A DNA microarray 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). These can be a short section of a gene or other DNA
* element that are used to hybridize a cDNA or cRNA 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. Since an array can contain tens of thousands
* of probes, a microarray experiment can accomplish many genetic tests in
* parallel. Therefore arrays have dramatically accelerated many types of
* investigation.
*
* In standard microarrays, the probes are synthesized and then attached via
* surface engineering to a solid surface by a covalent bond to a chemical
* matrix (via epoxy-silane, amino-silane, lysine, polyacrylamide or others).
* The solid surface can be glass or a silicon chip, in which case they are
* colloquially known as an Affy chip when an Affymetrix chip is used.
* Other microarray platforms, such as Illumina, use microscopic beads,
* instead of the large solid support. Alternatively, microarrays can be
* constructed by the direct synthesis of oligonucleotide probes on solid
* surfaces. DNA arrays are different from other types of microarray only
* in that they either measure DNA or use DNA as part of its detection system.
*
* DNA microarrays can be used to measure changes in expression levels,
* to detect single nucleotide polymorphisms (SNPs), or to genotype or
* resequence mutant genomes (see uses and types section). Microarrays
* also differ in fabrication, workings, accuracy, efficiency, and cost
* (see fabrication section). Additional factors for microarray experiments
* are the experimental design and the methods of analyzing the data.
*
* @author Haifeng Li
*/
package smile.data.parser.microarray;