Quantile Normalization to a Reference Distribution
Quantile normalization based upon a reference distribution. This function normalizes a matrix of data (typically Affy probe level intensities).
normalize.AffyBatch.normalize2Reference( abatch, type = c("separate", "pmonly", "mmonly", "together"), ref = NULL)
- A string specifying how the normalization should be applied. See details for more.
- A vector of reference values. See details for more.
This method is based upon the concept of a quantile-quantile
plot extended to n dimensions. No special allowances are made for
outliers. If you make use of quantile normalization either through
please cite Bolstad et al, Bioinformatics (2003).
The type argument should be one of
"separate","pmonly","mmonly","together" which indicates whether
to normalize only one probe type (PM,MM) or both together or separately.
The function uses the data supplied in
ref to use as the reference
distribution. In other words, the PMs in
abatch will be normalized
to have the same distribution as the data in
NULL, the normalizing takes place using the average quantiles
of the PM values in
abatch (just as in
- A normalized
Bolstad, B (2001) Probe Level Quantile Normalization of High Density Oligonucleotide Array Data. Unpublished manuscript
Bolstad, B. M., Irizarry R. A., Astrand, M, and Speed, T. P. (2003) A Comparison of Normalization Methods for High Density Oligonucleotide Array Data Based on Bias and Variance. Bioinformatics 19(2) ,pp 185-193.
# first, let affy/expresso know that the method exists # normalize.AffyBatch.methods <- c(normalize.AffyBatch.methods, "normalize2Reference") # example not run, as it would take a while # RawData <- ReadAffy(celfile.path=FilePath) # Batch1Step1 <- bg.correct(RawData, "rma") # Batch1Step2 <- normalize.AffyBatch.quantiles(Batch1Step1) # referencePM <- pm(Batch1Step2)[,1] # Batch1Step3 <- computeExprSet(Batch1Step2, "pmonly", "medianpolish") # Batch2Step1 <- bg.correct(RawData2, "rma") # Batch2Step2 <- normalize.AffyBatch.normalize2Reference(Batch2Step1, ref = referencePM) # Batch2Step3 <- computeExprSet(Batch2Step2, "pmonly", "medianpolish")