Up: Component summary Function

AffyNormalization

Reads in Affymetrix gene expression microarrays and compares various normalization methods.

Version 1.0
Bundle microarray
Categories Affy Data Import Normalization
Authors Marko Laakso (Marko.Laakso@Helsinki.FI)
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Source files component.xml function.scala
Usage Example with default values

Inputs

Name Type Mandatory Description
affy AffyDirectory Mandatory Affymetrix source file directory for AffyReader
sampleNames CSV Mandatory Sample definitions for AffyReader

Outputs

Name Type Description
report Latex Comparison of various normalization methods and their results

Parameters

Name Type Default Description
cdf string (no default) Chip annotation file as defined in Bioconductor
sectionTitle string "Normalization of Affymetrix data" Title of the comparison document

Test cases

Test case Parameters IN
affy
IN
sampleNames
OUT
report
case1 properties affy sampleNames (missing)

cdf=HGU133A


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