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RankProdIt: A web-interactive Rank Products analysis tool

BACKGROUND: The first objective of a DNA microarray experiment is typically to generate a list of genes or probes that are found to be differentially expressed or represented (in the case of comparative genomic hybridizations and/or copy number variation) between two conditions or strains. Rank Prod...

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Detalles Bibliográficos
Autores principales: Laing, Emma, Smith, Colin P
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2930644/
https://www.ncbi.nlm.nih.gov/pubmed/20691047
http://dx.doi.org/10.1186/1756-0500-3-221
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author Laing, Emma
Smith, Colin P
author_facet Laing, Emma
Smith, Colin P
author_sort Laing, Emma
collection PubMed
description BACKGROUND: The first objective of a DNA microarray experiment is typically to generate a list of genes or probes that are found to be differentially expressed or represented (in the case of comparative genomic hybridizations and/or copy number variation) between two conditions or strains. Rank Products analysis comprises a robust algorithm for deriving such lists from microarray experiments that comprise small numbers of replicates, for example, less than the number required for the commonly used t-test. Currently, users wishing to apply Rank Products analysis to their own microarray data sets have been restricted to the use of command line-based software which can limit its usage within the biological community. FINDINGS: Here we have developed a web interface to existing Rank Products analysis tools allowing users to quickly process their data in an intuitive and step-wise manner to obtain the respective Rank Product or Rank Sum, probability of false prediction and p-values in a downloadable file. CONCLUSIONS: The online interactive Rank Products analysis tool RankProdIt, for analysis of any data set containing measurements for multiple replicated conditions, is available at: http://strep-microarray.sbs.surrey.ac.uk/RankProducts
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spelling pubmed-29306442010-09-01 RankProdIt: A web-interactive Rank Products analysis tool Laing, Emma Smith, Colin P BMC Res Notes Technical Note BACKGROUND: The first objective of a DNA microarray experiment is typically to generate a list of genes or probes that are found to be differentially expressed or represented (in the case of comparative genomic hybridizations and/or copy number variation) between two conditions or strains. Rank Products analysis comprises a robust algorithm for deriving such lists from microarray experiments that comprise small numbers of replicates, for example, less than the number required for the commonly used t-test. Currently, users wishing to apply Rank Products analysis to their own microarray data sets have been restricted to the use of command line-based software which can limit its usage within the biological community. FINDINGS: Here we have developed a web interface to existing Rank Products analysis tools allowing users to quickly process their data in an intuitive and step-wise manner to obtain the respective Rank Product or Rank Sum, probability of false prediction and p-values in a downloadable file. CONCLUSIONS: The online interactive Rank Products analysis tool RankProdIt, for analysis of any data set containing measurements for multiple replicated conditions, is available at: http://strep-microarray.sbs.surrey.ac.uk/RankProducts BioMed Central 2010-08-06 /pmc/articles/PMC2930644/ /pubmed/20691047 http://dx.doi.org/10.1186/1756-0500-3-221 Text en Copyright ©2010 Laing et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 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.
spellingShingle Technical Note
Laing, Emma
Smith, Colin P
RankProdIt: A web-interactive Rank Products analysis tool
title RankProdIt: A web-interactive Rank Products analysis tool
title_full RankProdIt: A web-interactive Rank Products analysis tool
title_fullStr RankProdIt: A web-interactive Rank Products analysis tool
title_full_unstemmed RankProdIt: A web-interactive Rank Products analysis tool
title_short RankProdIt: A web-interactive Rank Products analysis tool
title_sort rankprodit: a web-interactive rank products analysis tool
topic Technical Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2930644/
https://www.ncbi.nlm.nih.gov/pubmed/20691047
http://dx.doi.org/10.1186/1756-0500-3-221
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