filter an 'ExpressionSet' using different methods

Share:

Description

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

Usage

1
  Filter(object, numChip=1, bg=0, range=0, iqrPct=0)

Arguments

object

an 'ExpressionSet'

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.

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.

Value

a filtered 'ExpressionSet'

Author(s)

Xiwei Wu xwu@coh.org, Xuejun Arthur Li xueli@coh.org

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
data(testData)
normaldata<-pre.process("rma",testData)

##At least one chip is greater than 4
filtered.1<-Filter(normaldata, numChip=1, bg=4)  

##At least one chip is greater than 4 and range >0.5
filtered.2<-Filter(normaldata, numChip=1, bg=4, range=0.5)  

##range >0.5 and IQR > 20percentile
filtered.3<-Filter(normaldata, range=0.5, iqrPct=0.2)