probeR {ProbeR}R Documentation

Calculate the reliability of one gene

Description

calculate the reliability of one gene using summary variance and probe data variance

Usage

probeR(summary.value, probe.value)

Arguments

summary.value the summary values of a specific gene for all the chips
probe.value the probe level data of a specific gene. It is a matrix that the number of row is the number of probes and the number of column is the number of chips

Value

summary.var the variance of the summary values
probe.var the variance of the probe level data
probe.n the number of probes
reliability the reliability


...

Author(s)

Eun-Kyung Lee, Dianne Cook, Heike Hofmann, Maneesha Aluru, and Steve Rodermel

References

Using Reliability with Gene Expression Models

See Also

probeR.wholegene, ~~~

Examples

library(affy)
data(affybatch.example)
eset<-expresso(affybatch.example,bg.correct=FALSE,normalize.method="quantiles",pmcorrect.method="pmonly",summary.method="medianpolish")
data.summary<-exprs(eset)
probe.norm<-normalize.AffyBatch.quantiles(affybatch.example,type="pmonly")
data.probe<-log(probes(probe.norm),base=2)
summary.value<-data.summary[1,]
probe.value<-data.probe[1:16,]
probeR(summary.value,probe.value)
data.rel<-probeR.wholegene(data.summary,data.probe)


[Package ProbeR version 2.0 Index]