affy

Submitted by covingto on Wed, 04/20/2011 - 15:05

Widgets for reading in and manipulating Affymetrix gene expression microarray data using the Bioconductor packages.

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Red-R Version:

Red-R-1.85b

Red-R Package Version:

1.21

Package Download:

	Widget	Description
	Affy RNA Degradation	Calculates the degradation of RNA from a set of Affy data.
	Bio Settings	Sets global settings to some commonly used biological settings.
	Biweight	Performs biweight data analysis on a dataset.
	Calculate Toptable	Generates a toptable of differentially expressed genes given a RMArrayLM model fit
	ComBat	Performs comBat adjustment of array data to compensate for batch effects. This widget will accept either two data tables representing the normalized expression values and the batch designations or a combination of file names representing the same.
	Create GO Analysis
	Differential Expression	Generates a differential expression model for data.
	Display GO Enrichment
	FDR Adjust
	Gene Selector	Filter Expression data for a set of genes and aggregates the probes into a single value.
	GO Analysis
	Local Pooled Error
	Normalize Affy Data	This widget normalizes gene expression data contained in an affy dataset.
	Pathway Enrichment	Performs Pathway Analysis on a genelist or subset (must specify gene list as either a full list or a subset on connecting)
	Plot Affy Data	Plots a summary of affy data.
	Plot RNA Degradation
	Present Calls	Calculates differential expression of genes from an eSet object
	Read CEL	Read in collections of CEL files from a directory into the Red-R session.
	Significance Criteria	Calculates differential expression of genes from an eSet object
	Sumarize RNA Degradation
	Volcanoplot	Generates a volcano plot of affy data.
	Write eSet	Writes an eSet to a tab delimited file.

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