RT Journal Article
T1 ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data
A1 Perkins, James Richard
A1 Dawes, John M
A1 McMahon, Steve B
A1 Bennett, David LH
A1 Orengo, Christine A.
A1 Kohl, Matthias
K1 Transcripción genética
K1 Genética molecular
AB 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.htmlConclusions: 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.
PB BMC
YR 2012
FD 2012-07
LK https://hdl.handle.net/10630/34467
UL https://hdl.handle.net/10630/34467
LA eng
NO Perkins, J.R., Dawes, J.M., McMahon, S.B. et al. ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data. BMC Genomics 13, 296 (2012). https://doi.org/10.1186/1471-2164-13-296
DS RIUMA. Repositorio Institucional de la Universidad de Málaga
RD 19 ene 2026