probeR.parallel.plot {ProbeR} | R Documentation |
Parallel coordinate plot of summary value and probe level data is very useful to explore the probe level data with summary value gene by gene.
probeR.parallel.plot(affy.ID,data.summary, data.probe)
affy.ID |
affymetrix id |
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. |
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) probeR.parallel.plot("D78156_at",data.summary,data.probe)