getBackground: Get background estimates for a NanoString RccSet

In NanoStringQCPro: Quality metrics and data processing methods for NanoString mRNA gene expression data

Description

Returns background estimates for a NanoString RccSet object. The function depends upon correct annotation in the RccSet: if the bgReference argument is set to "blanks", it expects blank measurements (i.e., water runs) to have their phenoData SampleType set to the value indicating blanks or an error will be thrown. (See getBlankLabel(); normally this value would have been set using an argument to newRccSet()). If bgReference is set to "negatives", then it expects to find the negative control probes via CodeClass == "Negative". If set to "both", it expects both of the above and will calculate initial background estimates using an algorithm that mimics the implementation in NanoString's nSolver Analysis Software (see the nSolverBackground() man page for details on the algorithm).

Usage

## S4 method for signature 'RccSet'
getBackground(rccSet, bgReference = c("both", "blanks",
  "negatives"), summaryFunction = "median", stringency = 0,
  nSolverBackground.shrink = TRUE, nSolverBackground.w1 = 2.18,
  inputMatrix = c("posCtrlData", "exprs"))

Arguments

rccSet	NanoString RccSet object.
bgReference	Measurements to use for background estimates: one of "blanks" (for blank samples), "negatives" (for negative control probes), or "both". Blanks are assumed to be indicated as in the description above.
summaryFunction	Summary function for background measurements (e.g. "mean" or "median"). User-defined functions similar to these can be specified here as well.
stringency	Factor by which deviation (SD or MAD) of the summarization output will be multiplied to obtain final background estimates.
nSolverBackground.shrink	Value to use for the 'shrink' argument to nSolverBackground().
nSolverBackground.w1	Value to use for the 'w1' argument to nSolverBackground().
inputMatrix	Name of the matrix in the RccSet's assayData to use as input for calculating background estimates (one of "exprs" or "posCtrlData"). If posCtrlData is specified but not present in the assayData, an error will be generated.

Value

A matrix containing background estimates for a NanoString RccSet object.

Author(s)

Dorothee Nickles

See Also

subtractBackground

Examples

data(example_rccSet)

## Calculate probe-specific background based on negative control probes
bg <- getBackground(example_rccSet, bgReference="negatives", summaryFunction="mean",
    inputMatrix="exprs")

## Calculate sample-specific background based on blanks
bg <- getBackground(example_rccSet, bgReference="blanks", inputMatrix="exprs")

## Calculate background that is both sample- and probe-specific
bg <- getBackground(example_rccSet, bgReference="both", stringency=1,
    inputMatrix="exprs")

NanoStringQCPro documentation built on Nov. 8, 2020, 8:11 p.m.