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Reference: Perkins, JR, Dawes, JM, McMahon, SB et al., (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.Citable link to this page:

 

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.

Peer Review status:Peer reviewedPublication status:PublishedVersion:Publisher's version Funder: Wellcome Trust   Funder: European Commission's Sixth Framework Programme   Notes:© 2012 Perkins et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Bibliographic Details

Publisher: BioMed Central Ltd.

Publisher Website: http://www.biomedcentral.com/

Journal: BMC genomicssee more from them

Publication Website: http://www.biomedcentral.com/bmcgenomics/

Issue Date: 2012-1

pages:296Identifiers

Urn: uuid:e9750711-8dbb-4650-acad-92330a5e019a

Source identifier: 365753

Eissn: 1471-2164

Doi: https://doi.org/10.1186/1471-2164-13-296

Issn: 1471-2164 Item Description

Type: Journal article;

Language: eng

Version: Publisher's versionKeywords: Software Algorithms Real-Time Polymerase Chain Reaction Tiny URL: pubs:365753

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Author: Perkins, JR - - - Dawes, JM - - - McMahon, SB - - - Bennett, DL - institutionUniversity of Oxford Oxford, MSD, Clinical Neuroscie

Source: https://ora.ox.ac.uk/objects/uuid:e9750711-8dbb-4650-acad-92330a5e019a



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