affy (version 1.50.0)

writeFit: Function to output annotated fit data from limma

Description

This function is designed to take an ExpressionSet an annotation package and an lmFit object, and output an annotated text file containing t-statistics, p-values, and fold change data for all contrasts.

Usage

writeFit(fit, annotation = NULL, eset, touse = c("symbol", "genename",
  "accnum", "entrezid", "unigene"))

Arguments

fit

A lmFit object, created by the limma package.

annotation

An annotation package, specific for the chip used in the analysis.

eset

An ExpressionSet object containing expression values.

touse

Character vector of BiMaps from annotation package. As an example, if the annotation package is the hgu133plus2.db package, then 'symbol' refers to the hgu133plus2SYMBOL BiMap.

Value

• A data.frame is returned.

Details

This function is designed to output annotation data as well as statistics (p-values, fold change, t-statistics) for all probes on a chip.

See Also

write.fit