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affymetrix [2010/05/30 10:38]
dmontaner
affymetrix [2017/05/24 10:36] (current)
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 +====== Affymetrix ======
 +
 +[[Affymetrix]] is a microarray manufacturer: http://www.affymetrix.com
 +
 +
 +[[Affymetrix]] manufactures **one color** microarrays. Their chips consist of small DNA fragments, referred to as **probes**, synthesized at specific locations (spots) on a coated quartz surface. Every **probe** in an [[Affymetrix]] microarray has **25** nucleotide length. It is designed to determine whether or not the complementary sequence of an RNA or DNA molecule is present in the sample, and to quantify its concentration. 
 +
 +[[Affymetrix]] uses a //set// probes to interrogate each genomic feature like genes or exons. Such group of probes is called **probe-set** and can be averaged into a 
 +single measurement for the genomic feature.
 +
 +In //classical// [[Affymetrix]] arrays, for each probe that //perfectly// matches ([[PM]]) its target sequence, [[Affymetrix]] also builds a paired //mismatch// probe ([[MM]]). The **mismatch probe** contains a change in the nucleotide located directly in the middle of the 25-base probe sequence and is designed to measure [[cross-hybridization|non specific hybridization]]. A prefect match probe and its mismatch are referred to as a **probe-pair**. Thanks to the [[MM]] probes, [[Affymetrix]] microarrays can be used to get a **present-absent** call for each gene, indicating whether it is present or not in the sample.
 +
 +Recently, [[Affymetrix]] has refined its technology and, among other changes, new microarrays do not follow the [[PM]]-[[MM]] design. In contrast, a group of probes which do not match biological sequences is used as **control** for all other [[PM]] probes. This design increases the amount of features that can be screened while keeping the possibility of getting **present-absent** calls for them.
 +
 +After scanning each array, [[Affymetrix]] software computes probe intensity data and saves them into a [[CEL]] file using a particular structure. Such [[CEL]] files are the starting point for the [[Affymetrix]] normalization module in [[Babelomics]]: your **[[raw data]]**.
 +
 +If you  are using an **standard** Affymetrix chip our tool will recognize the kind of array you are using and you will be able to normalize it. At the moment it is not possible to analyze **custom** [[Affymetrix]] arrays using [[Babelomics]].
 +
 +Many different algorithms have been proposed in the past years for normalizing [[Affymetrix]] microarray data. At the end, two of them become standards and are the ones available in [[Babelomics]]: 
 +  * [[http://biostatistics.oxfordjournals.org/cgi/content/abstract/4/2/249|RMA]]
 +  * [[http://www.affymetrix.com/support/technical/technotes/plier_technote.pdf|PLIER]]
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