frma (version 1.24.0)

barcode: Gene Expression Barcode

Description

This function converts expression values produced via fRMA to a gene expression barcode.

Usage

barcode(object, platform=NULL, mu=NULL, tau=NULL, cutoff=6.5, output="binary")

Arguments

object

a vector or matrix of expression values or an ExpressionSet or frmaExpressionSet produced by frma

platform

the platform of the input data. One of GPL96, GPL570, GPL571, GPL1261, GPL6244, GPL6246. Required if object is a vector or matrix and either mu or tau is NULL.

mu

the mean of the unexpressed distribution. If NULL then precomputed values are used if possible.

tau

the standard deviation of the unexpressed distribution. If NULL then precomputed values are used if possible.

cutoff

the lod score cutoff used if output is binary.

output

the desired values to be returned. Options are: p-value, z-score, lod, or binary.

Value

A matrix containing the type of output specified by the output parameter. The option binary creates a gene expression barcode where 1s denote expressed genes and 0s denote unexpressed genes. The option p-value returns the p-values for the expression values under the unexpressed distribution. The option lod returns the LOD scores for expression values under the unexpressed distribution. The option z-score returns the z-scores for the expression values under the unexpressed distribution.

Examples

  library(frma)
  library(frmaExampleData)
  data(AffyBatchExample)
  object <- frma(AffyBatchExample)
  bc <- barcode(object)