How do I create an ExpressionSet in R?

How do I create an ExpressionSet in R?

Instructions

1. Create a new ExpressionSet object using the function ExpressionSet .
2. Pass the expression matrix to the assayData argument.
3. Pass the phenotype data frame to the phenoData argument.
4. Pass the feature data frame to the featureData argument.

What is an Expression set in r?

GEOQuery returns data in an object of the ExpressionSet class. You can think of an ExpressionSet class as a container designed to combine multiple sources of information from a gene expression experiment into a single object.

Which is an example of an expressionet instance?

Directly extends class eSet. ExpressionSet instances are usually created through ExpressionSet (). Contains matrices with equal dimensions, and with column number equal to nrow (phenoData). assayData must contain a matrix exprs with rows representing features (e.g., probe sets) and columns representing samples.

How to create an expression in expressionset function?

## Instance creation ExpressionSet (assayData, phenoData=annotatedDataFrameFrom (assayData, byrow=FALSE), featureData=annotatedDataFrameFrom (assayData, byrow=TRUE), experimentData=MIAME (), annotation=character (), protocolData=annotatedDataFrameFrom (assayData, byrow=FALSE).) A matrix of expression values, or an environment.

How is the assay data retrieved in expressionset?

The assay data can be retrieved with exprs (). When assayData is an environment, it contains identically dimensioned matrices like that described in the previous paragraph. One of the elements of the environment must be named ‘exprs’; this element is returned with exprs ().

How is the expressionset class used in Bioconductor?

The ExpressionSet class is designed to combine several di erent sources of information into a single convenient structure. An ExpressionSet can be manipulated (e.g., subsetted, copied) conveniently, and is the input or output from many Bioconductor functions.