sortedIqrPlot: Minimal box plot of samples, which get ordered optionally by...

In ffpe: Quality assessment and control for FFPE microarray expression data

Description

This plots only the 25th to 75th percentile of expression intensities (Interquartile Range), sorted from smallest to largest IQR. This modification is more readable than a regular boxplot for large sample sizes. An optional batch variable may be specified, so that the sorting is done within each batch.

Usage

sortedIqrPlot(data.obj, batchvar = rep(1, ncol(data.obj)), dolog2=FALSE, ...)
      ## S4 method for signature 'LumiBatch'
sortedIqrPlot(data.obj, batchvar = rep(1, ncol(data.obj)), dolog2=FALSE, ...)
      ## S4 method for signature 'AffyBatch'
sortedIqrPlot(data.obj, batchvar = rep(1, ncol(data.obj)), dolog2=FALSE, ...)
      ## S4 method for signature 'matrix'
sortedIqrPlot(data.obj, batchvar = rep(1, ncol(data.obj)), dolog2=FALSE, ...)

Arguments

data.obj	An object of class LumiBatch, AffyBatch, AffyBatch, or matrix. This should contain raw, unnormalized, expression intensities.
batchvar	Optional integer batch variable. If specified, samples will be sorted within batches only. Default is to assume a single batch for all data.
dolog2	If TRUE, data will be log2-transformed before plotting. Default is FALSE.
...	Optional arguments passed on to the plot() function.

Details

Function will be generally called for the side-effect of producing a plot of sorted IQRs, but if the output is redirected it also produces the IQRs.

Value

If the output is redirected, e.g.:

output <- sortedIqrPlot()

the function will return the IQR of each sample.

Author(s)

Levi Waldron <[e-mail]>

References

Under review.

See Also

sampleQC

Examples

library(ffpeExampleData)
data(lumibatch.GSE17565)
sortedIqrPlot(lumibatch.GSE17565,main="GSE17565")

ffpe documentation built on Nov. 8, 2020, 7:50 p.m.