Generate an expression value from the probes informations
Generate an expression from the probes
generateExprVal.method.avgdiff(probes, ...) generateExprVal.method.medianpolish(probes, ...) generateExprVal.method.liwong(probes, ...) generateExprVal.method.mas(probes, ...)
probes |
a matrix of probe intensities with rows representing
probes and columns representing samples. Usually |
... |
extra arguments to pass to the respective function. |
A list containing entries:
exprs |
The expression values. |
se.exprs |
The standard error estimate. |
data(SpikeIn) ##SpikeIn is a ProbeSets probes <- pm(SpikeIn) avgdiff <- generateExprVal.method.avgdiff(probes) medianpolish <- generateExprVal.method.medianpolish(probes) liwong <- generateExprVal.method.liwong(probes) playerout <- generateExprVal.method.playerout(probes) mas <- generateExprVal.method.mas(probes) concentrations <- as.numeric(sampleNames(SpikeIn)) plot(concentrations,avgdiff$exprs,log="xy",ylim=c(50,10000),pch="a",type="b") points(concentrations,2^medianpolish$exprs,pch="m",col=2,type="b",lty=2) points(concentrations,liwong$exprs,pch="l",col=3,type="b",lty=3) points(concentrations,playerout$exprs,pch="p",col=4,type="b",lty=4) points(concentrations,mas$exprs,pch="p",col=4,type="b",lty=4)
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