qPCRBatch-class:
Class qPCRBatch
Description
Class to Contain and Describe raw and normalised qPCR Data, as Cq or delta-Cq values. Extends eSet
Creating Objects
new("qPCRBatch")Slots
assayData:- Object of class
AssayData containing the raw data,
which will be at minimum a matrix of Cq values. This
slot can also hold a matrix of well.info values if these are present in the input file read
in by read.qPCR or read.taqman
phenoData:- Object of class
AnnotatedDataFrame
containing phenotypic data for the samples.
annotation- A character string identifying the
annotation that may be used for the
qPCRBatch
instance.
protocolData:- Object of class
AnnotatedDataFrame
containing protocol data for the samples.
featureData- Object of class
AnnotatedDataFrame
containing feature-level (e.g., probeset-level) information.
experimentData:- Object of class "MIAME" containing
experiment-level information.
.__classVersion__:- Object of class
Versions
describing the R and Biobase version number used to create the
instance. Intended for developer use.
Methods
- exprs
signature(object = "qPCRBatch"): extracts the Cq
expression matrix.- exprs<-
signature(object = "qPCRBatch", value = "matrix"):
replaces the Cq expression matrix.- se.exprs
signature(object = "qPCRBatch"): extracts the
expression matrix with SDs of Cq values.- se.exprs<-
signature(object = "qPCRBatch", value = "matrix"):
replaces the expression matrix with SDs of Cq values.- exprs.well.order
signature(object = "qPCRBatch"): extracts the Cq
well order matrix (if it exists).- exprs.well.order<-
signature(object = "qPCRBatch", value = "matrix"):
replaces the Cq well order matrix.- effs
signature(object = "qPCRBatch"): extracts the efficiency
matrix (if it exists).- effs<-
signature(object = "qPCRBatch", value = "matrix"):
replaces the efficiency matrix.- se.effs
signature(object = "qPCRBatch"): extracts the matrix
with the standard errors/deviations of the efficiencies (if it exists).- se.effs<-
signature(object = "qPCRBatch", value = "matrix"):
replaces the matrix with the standard errors/deviations of the efficiencies.
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.