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: 
application/zip iconaffy-1.21.zip
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.