title: ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data.
abstract: BACKGROUND
  Measuring gene transcription using real-time reverse transcription polymerase chain reaction (RT-qPCR) technology is a mainstay of molecular biology. Technologies now exist to measure the abundance of many transcripts in parallel. The selection of the optimal reference gene for the normalisation of this data is a recurring problem, and several algorithms have been developed in order to solve it. So far nothing in R exists to unite these methods, together with other functions to read in and normalise the data using the chosen reference gene(s).
  
  
  RESULTS
  We have developed two R/Bioconductor packages, ReadqPCR and NormqPCR, intended for a user with some experience with high-throughput data analysis using R, who wishes to use R to analyse RT-qPCR data. We illustrate their potential use in a workflow analysing a generic RT-qPCR experiment, and apply this to a real dataset. Packages are available from http://www.bioconductor.org/packages/release/bioc/html/ReadqPCR.htmland http://www.bioconductor.org/packages/release/bioc/html/NormqPCR.html
  
  
  CONCLUSIONS
  These packages increase the repetoire of RT-qPCR analysis tools available to the R user and allow them to (amongst other things) read their data into R, hold it in an ExpressionSet compatible R object, choose appropriate reference genes, normalise the data and look for differential expression between samples.
authors: Institute of Structural and Molecular Biology, University College of London, London, UK. j.perkins@ucl.ac.uk
authors: James R
authors: JR
authors: Perkins
authors: John M
authors: JM
authors: Dawes
authors: Steve B
authors: SB
authors: McMahon
authors: David L H
authors: DL
authors: Bennett
authors: Christine
authors: C
authors: Orengo
authors: Matthias
authors: M
authors: Kohl
mesh_terms: D000465:Algorithms; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D012984:Software