View source for Normalize Affymetrix experiment and control (analysis)

;Analysis title
:[[File:Data-Normalize-Affymetrix-experiment-and-control-icon.png]] Normalize Affymetrix experiment and control
;Provider
:[[geneXplain GmbH]]
;Class
:{{Class|com.genexplain.analyses.AffymetrixNormalizeAndSplit}}
;Plugin
:[[Com.genexplain.analyses (plugin)|com.genexplain.analyses (geneXplain analyses)]]

==== Description ====
This procedure takes Affymetrix CEL files as input and returns normalized data. Normalization is carried out using methods in the Bioconductor AFFY package. Individual CEL files are assigned to either test condition (experiment, study, treatment) or control condition.

The first step normalizes test and control measurements altogether and calculates normalized signal values. The default normalization method is MAS5. Several other methods are available for selection.

Next, the table comprising both test and control values is split yielding two tables for each experiment group. The resulting tables, "Experiment normalized" and "Control normalized", can be applied in subsequent next workflows, such as Compute differentially expressed genes and Gene set enrichment analysis.

==== Parameters: ====

* '''Experiment files''' – Files with experimental data
* '''Control files''' – Control files
* '''Method''' – Method
* '''Background correction''' (expert) – Background correction
* '''Normalization method''' (expert) – Normalization method
* '''PM correction''' (expert) – PM correction
* '''Summarization''' (expert) – Summarization
* '''CDF version''' (expert) – Specific CDF version for normalization, use <nowiki>'</nowiki>none<nowiki>'</nowiki> for default one
* '''Result logarithm base''' – Logarithm base of result
* '''Output table test data''' – Output table with test data
* '''Output table control data''' – Output table with control data

[[Category:Analyses]]
[[Category:Data (analyses group)]]
[[Category:GeneXplain analyses]]
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