plotVarMean: Constructs scatter plot to compare the effects of two...

Description Usage Arguments Details Value Author(s) References See Also Examples


This function makes a scatter plot which serves as a useful exploratory tool in evaluating whether one normalization algorithm has been more effective than another on a given qPCR dataset.


plotVarMean(qpcrBatch1, qpcrBatch2, normTag1 = "Normalization Type1", normTag2 = "Normalization Type2", ...)



A qpcrBatch object.


A qpcrBatch object.


Character string denoting what normalization algorithm was used for this data set.


Character string denoting what normalization algorithm was used for this data set.


Further arguments can be supplied to the plot function.


For each gene, the function plots its log-transformed ratio of its expression variance in one normalized dataset versus another normalized dataset, i.e. let Gij be the variance of the expression values of gene i that have been normalized with method j. We plot the natural log-transformed ratio of Gij to Gik on the y-axis, and the average expression of gene i on the x-axis for all genes. /cr The red curve represents a smoothed lowess curve that has been fitted to reflect the overall trend of the data. When the red curve drops below y = 0 (the blue dotted line) we know that method j effects a greater reduction in the variation of the data over method k. Similarly, when the red curve is above y = 0, method k is more effective in reducing the variation in the data than method j. If the data from both methods have similar variances then the red curve should remain at y = 0. Bolstad et al. (2003) originally used these plots for variance comparisons of different normalization methods for high density oligonucleotide array data.


A plot object.


Jess Mar


Bolstad B et al. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics, 2003.

See Also



  # data(qpcrBatch.object)
  # <- normQpcrRankInvariant(qpcrBatch.object, 1) 
  # <- normQpcrQuantile(qpcrBatch.object)
  # plotVarMean(,, normTag1="Rank-Invariant", normTag2="Quantile", main="Comparing Two Data-driven Methods")  

Search within the qpcrNorm package
Search all R packages, documentation and source code

Questions? Problems? Suggestions? or email at

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.