NormqPCR (version 1.18.0)

replaceAboveCutOff: Replace Cq values with new value

Description

Replace Cq values above a given threshold with a new value

Usage

replaceAboveCutOff(qPCRBatch, ...)
"replaceAboveCutOff"(qPCRBatch, newVal=NA, cutOff=38)

Arguments

qPCRBatch

Expression set containing qPCR data.

...

Extra arguments, detailed below

newVal

The new value with which to replace the values above the cutoff

cutOff

the minimal threshold above which the values will be replaced

Value

qPCRBatch object with a new exprs slot

Details

Replaces values in the exprs slot of the qPCRBatch object that are above a threshold value with a new number

References

Perkins, JR, Dawes, JM, McMahon, SB, Bennett, DL, Orengo, C, Kohl, M (2012). ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data. BMC Genomics, 13, 1:296.

Examples

  path <- system.file("exData", package = "NormqPCR")
  taqman.example <- file.path(path, "example.txt")
  qPCRBatch.taqman <- read.taqman(taqman.example)
  exprs(qPCRBatch.taqman)["Ccl20.Rn00570287_m1",]
  qPCRBatch.taqman.replaced <- replaceAboveCutOff(qPCRBatch.taqman, newVal = NA, cutOff = 35)
  exprs(qPCRBatch.taqman.replaced)["Ccl20.Rn00570287_m1",]