2026-06-05T17:30:49Zhttps://riuma.uma.es/rest/oai/requestoai:riuma.uma.es:10630/344672026-02-03T11:13:15Zcom_10630_2254col_10630_37953
RIUMA. Repositorio Institucional de la Universidad de Málaga
author
Perkins, James Richard
author
Dawes, John M
author
McMahon, Steve B
author
Bennett, David LH
author
Orengo, Christine A.
author
Kohl, Matthias
2024-10-08T07:31:58Z
2024-10-08T07:31:58Z
2012-07
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
https://hdl.handle.net/10630/34467
10.1186/1471-2164-13-296
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.
eng
Atribución-NoComercial 4.0 Internacional
Transcripción genética
Genética molecular
ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data
journal article
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URL
https://riuma.uma.es/bitstreams/1156423f-5aec-463f-8867-143ec561afbf/download
File
MD5
b8fc235d3c26d04bbb3908abba3ad586
879914
application/pdf
NormqPCR.pdf