ComputeNRQs {NormqPCR} | R Documentation |
This function computes normalized relative quantities (NRQs) for a qPCRBatch
.
ComputeNRQs(qPCRBatch, ...) ## S4 method for signature 'qPCRBatch' ComputeNRQs(qPCRBatch, hkgs)
qPCRBatch |
an object of class |
hkgs |
Names of reference/housekeeping genes. |
... |
other parameters to be passed to downstream methods. |
Allows the user to normalized relative quantities as defined in Hellemanns et al. (2007).
Object of class "qPCRBatch"
.
Nor Izayu Abdul Rahman, Matthias Kohl Matthias.Kohl@stamats.de
Jan Hellemans, Geert Mortier, Anne De Paepe, Frank Speleman and Jo Vandesompele (2007). qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biology, 8:R19
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.
## Example data path <- system.file("exData", package = "ReadqPCR") qPCR.example <- file.path(path, "qPCR.example.txt") Cq.data <- read.qPCR(qPCR.example) ## combine technichal replicates Cq.data1 <- combineTechRepsWithSD(Cq.data) ## add efficiencies Effs <- file.path(path, "Efficiencies.txt") Cq.effs <- read.table(file = Effs, row.names = 1, header = TRUE) rownames(Cq.effs) <- featureNames(Cq.data1) effs(Cq.data1) <- as.matrix(Cq.effs[,"efficiency",drop = FALSE]) se.effs(Cq.data1) <- as.matrix(Cq.effs[,"SD.efficiency",drop = FALSE]) ## res <- ComputeNRQs(Cq.data1, hkgs = c("gene_az", "gene_gx")) ## NRQs exprs(res) ## SD of NRQs se.exprs(res)