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affy (version 1.50.0)

tableFilt: Filter a topTable object

Description

This function is designed to filter genes from a topTable object based on p-value and/or fold change. This is an internal function and is not intended to be called by thte end user.

Usage

tableFilt(fit, coef = 1, number = 30, fldfilt = NULL, pfilt = NULL,
  adjust = "fdr")

Arguments

fit
An MArrayLM object, resulting from a call to eBayes
coef
The contrast to be extracted into the topTable. See ?topTable for more information.
number
The number of genes to output. Only used if both foldfilt and pfilt are NULL.
fldfilt
The absolute value of fold difference to filter on. This assumes the data are log transformed.
pfilt
The p-value to filter on.
adjust
The multiplicity adjustment to use. Options are '"bonferroni"', '"holm"', '"hochberg"', '"hommel"', '"fdr"' and '"none"'. If '"none"' then the p-values are not adjusted. A 'NULL' value will result in the default adjustment method, which is '"fdr"'.

Value

  • Returns a data.frame containing the selected genes.