Difference between revisions of "Affymetrix normalization (analysis)"

From BioUML platform
Jump to: navigation, search
(Plugin name added)
(Automatic synchronization with BioUML)
 
(5 intermediate revisions by one user not shown)
Line 1: Line 1:
 
;Analysis title
 
;Analysis title
:[[File:Data-Affymetrix-normalization-icon.png]] Affymetrix normalization
+
:[[File:Microarray-normalization-Affymetrix-normalization-icon.png]] Affymetrix normalization
 
;Provider
 
;Provider
 
:[[Institute of Systems Biology]]
 
:[[Institute of Systems Biology]]
 +
;Class
 +
:{{Class|ru.biosoft.analysis.CELNormalization}}
 
;Plugin
 
;Plugin
:ru.biosoft.analysis (Common methods of data analysis plug-in)
+
:[[Ru.biosoft.analysis (plugin)|ru.biosoft.analysis (Common methods of data analysis plug-in)]]
  
 
=== Affymetrix Normalization ===
 
=== Affymetrix Normalization ===
Line 26: Line 28:
  
 
[[Category:Analyses]]
 
[[Category:Analyses]]
[[Category:Data (analyses group)]]
+
[[Category:Microarray normalization (analyses group)]]
 
[[Category:ISB analyses]]
 
[[Category:ISB analyses]]
 
[[Category:Autogenerated pages]]
 
[[Category:Autogenerated pages]]

Latest revision as of 18:15, 9 December 2020

Analysis title
Microarray-normalization-Affymetrix-normalization-icon.png Affymetrix normalization
Provider
Institute of Systems Biology
Class
CELNormalization
Plugin
ru.biosoft.analysis (Common methods of data analysis plug-in)

[edit] Affymetrix Normalization

Normalization of Affymetrix CEL files based on the functions of the Bioconductor AFFY package.

[edit] Parameters:

  • CEL file - the path to the CEL file.
  • Method (normalize AFFY function) - A generic function which normalizes microarray data. Normalization is intended to remove from the intensity measures any systematic trends which arise from the microarray technology rather than from differences between the probes or between the target RNA samples hybridized to the arrays.
  • Background Correction (bgcorrect.method) - the name of the background adjustment method.
  • Normalization method (normalize.method) - the normalization method to use.
  • PM correction (pmcorrect.method) - the name of the PM adjustment method.
  • Summarization (summary.method) - the method used for the computation of expression values.
  • CDF version - version of Affymetrix CDF file.
  • Output name - the name of the output data file.

Original names of the AFFY functions used for analysis are shown in parentheses. For a detailed description of these functions see the AFFY reference manual.

Note: Before the CEL normalization is started you need to install R and Rserve on your computer. For more information on installing, please visit R-project website.

Personal tools
Namespaces

Variants
Actions
BioUML platform
Community
Modelling
Analysis & Workflows
Collaborative research
Development
Virtual biology
Wiki
Toolbox