cy3GenerateRef: Generate Cy3 empirical reference
In pkimes/upbm: Tools for the analysis of universal protein binding microarrays

Description Usage Arguments Details Value Author(s)

Given a collection of Cy3 scans, this function estimates an empirical reference distribution of expected Cy3 intensities per probe. Scans must all be for the same array design. For each probe, the mean, median, MAD, and standard deviation of the log2 intensities is computed across all Cy3 scans.

The estimated reference distributions can be passed to cy3FitEmpirical with a PBMExperiment of Cy3 scan intensities to determine probe-level outliers and scaling factors for the individual Cy3 scans relative to the reference.

cy3GenerateRef(
  cy3pe,
  assay = SummarizedExperiment::assayNames(cy3pe)[1],
  offset = 1L,
  register = TRUE
)

`cy3pe`	a PBMExperiment object containing Cy3 intensity data.
`assay`	a numeric index or string specifying the intensity assay. (default = `SummarizedExperiment::assayNames(cy3pe)[1]`)
`offset`	a numeric offset to add to intensities before log2 transforming to prevent NAs with zero intensities. (default = `1L`)
`register`	a logical value whether to scale intensities across samples. (default = TRUE)

By default, samples are first scaled to have a common median intensity, and the reference probe-level intensities are computed on the log2 scale.

Scaling is performed such that the median intensity of each sample is equal to the median sample-median intensity of the original intensities. This multiplicative scaling is equivalent to an additive shift on the log2 scale. This behavior can be turned off by specifying register = FALSE.

The probe-level summary metrics are calculated on the log2 scale because Cy3 scans will be used for filtering and scaling, actions which require examining fold changes and ratios rather than raw intensity differences.

PBMExperiment object with Cy3 probe-level reference metrics.

Patrick Kimes

pkimes/upbm documentation built on Oct. 17, 2020, 9:10 a.m.