Emmanuel Curis1,2,3, Cindie Courtin2, Pierre Alexis Geoffroy2,4, Jean-Louis Laplanche2, Bruno Saubaméa2, Cynthia Marie-Claire2. 1. Laboratoire de Biomathématiques, Faculté de Pharmacie de Paris, Université Paris Descartes, Sorbonne Paris Cité, Paris F-75006, France. 2. UMR S-1144 INSERM-Université Paris Descartes-Université Paris Diderot, Paris F-75006, France. 3. Service de Bioinformatique et Information Médicale, Hôpital Saint-Louis, AP-HP, Paris F-75012, France. 4. Pôle de Psychiatrie et de Médecine, Addictologique GH Saint-Louis - Lariboisière - F. Widal AP-HP, Paris F-75475, France.
Abstract
Motivation: RNA quantification experiments result in compositional data, however usual methods for compositional data analysis [additive log ratio (alr), centered log ratio (clr), isometric log ratio (ilr)] do not apply easily and give results difficult to interpret. To handle this, a method based on disjoint subgraphs in a graph whose nodes are the quantified RNAs is proposed. Edges in the graph are defined by lack of change in ratios of the corresponding RNAs between conditions. Results: The methods is suited for qRT-PCR and RNA-Seq data analyses, and leads to easy-to-interpret, graphical results and the identification of set of genes that share a similar behavior when the studied condition changes. For qRT-PCR data, it has better statistical properties than the common ΔΔCq method. Availability and implementation: Construction of all pairwise ratio analysis P-values matrix, and conversion into a graph was implemented in an R package, named SARP.compo. It is freely available for download on the CRAN repository. Example R script using the package are provided as Supplementary Material; the R package includes the data needed. One of these scripts reproduces the Figure 2 of this paper. Supplementary information: Supplementary data are available at Bioinformatics online.
Motivation: RNA quantification experiments result in compositional data, however usual methods for compositional data analysis [additive log ratio (alr), centered log ratio (clr), isometric log ratio (ilr)] do not apply easily and give results difficult to interpret. To handle this, a method based on disjoint subgraphs in a graph whose nodes are the quantified RNAs is proposed. Edges in the graph are defined by lack of change in ratios of the corresponding RNAs between conditions. Results: The methods is suited for qRT-PCR and RNA-Seq data analyses, and leads to easy-to-interpret, graphical results and the identification of set of genes that share a similar behavior when the studied condition changes. For qRT-PCR data, it has better statistical properties than the common ΔΔCq method. Availability and implementation: Construction of all pairwise ratio analysis P-values matrix, and conversion into a graph was implemented in an R package, named SARP.compo. It is freely available for download on the CRAN repository. Example R script using the package are provided as Supplementary Material; the R package includes the data needed. One of these scripts reproduces the Figure 2 of this paper. Supplementary information: Supplementary data are available at Bioinformatics online.