Description Usage Arguments Details Value Author(s) Examples
Create a filtered 'ExpressionSet' based on background, range, or interquartile range
1 |
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. |
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.
a filtered 'ExpressionSet'
Xiwei Wu xwu@coh.org, Xuejun Arthur Li xueli@coh.org
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)
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