probeR.wholegene {ProbeR} | R Documentation |
calculate the reliability of the whole genes using summary variance and probe data variance
probeR.wholegene(data.summary, data.probe)
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. |
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 |
...
Eun-Kyung Lee, Dianne Cook, Heike Hofmann, Maneesha Aluru, and Steve Rodermel
Using Reliability with Gene Expression Models
probeR
, ~~~
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)