probeR.wholegene {ProbeR}R Documentation

Calculate the reliability of the whole genes

Description

calculate the reliability of the whole genes using summary variance and probe data variance

Usage

probeR.wholegene(data.summary, data.probe)

Arguments

data.summary the summary values from the function exprs
data.probe the normalized probe level data. They should be normalized using the same method for the summary values. Also they should be the same probe level data calculating the summary values. If the user use RMA with PM values, this should be only PM values.

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, ~~~

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]