probeR {ProbeR} | R Documentation |
calculate the reliability of one gene using summary variance and probe data variance
probeR(summary.value, probe.value)
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 |
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.wholegene
, ~~~
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)