ArrayTools (version 1.32.0)

geneFilter: filter an ExpressionSet using different methods

Description

Create a filtered 'ExpressionSet' based on background, range, or interquartile range

Usage

geneFilter(object, pct = 0.1, numChip = ceiling(ncol(exprs(object)) * pct), bg = 4, range = 0, iqrPct = 0, output = FALSE, mydir = getwd())

Arguments

object

an ExpressionSet

pct

percentage

numChip

number of chips. If you would like to filter the ExpressionSet based on at least 3 chips greater than 1 (bg=1), then set numChip = 3

bg

background value. If you would like to filter the ExpressionSet based on at least 3 chips greater than 1, then set bg=1

range

range = max value - min value of each gene

iqrPct

interquartile percentage

output

if output = TRUE, output filtered data in the sepecified directory

mydir

the directory containing the filtered data

Value

a filtered ExpressionSet

Details

There are three filtering methods. The User can use either one, two, or three. 1). At least a certain number of chips (numChip) are greater than a given background (bg) 2). The range of the gene have to be greater than a given value (range) 3). Calulating the interquatile range (IQR) of each gene to create an IQR vector. Based on the given percentage (e.g. iqrPct=0.2), find the corresponding percentile. If IQR is less than percentile, the gene will be filtered

Examples

data(eSetExample)
filtered <- geneFilter(eSetExample)