writeFit: Function to output annotated fit data from limma

In jmacdon/affycoretools: Functions useful for those doing repetitive analyses with Affymetrix GeneChips

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.

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.

Value

A data.frame is returned.

Author(s)

James W. MacDonald <[e-mail]>

See Also

write.fit

jmacdon/affycoretools documentation built on Nov. 2, 2024, 1:29 a.m.