FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2004014148> ?p ?o ?g. }

• W2004014148 endingPage "e1003531" @default.
• W2004014148 startingPage "e1003531" @default.
• W2004014148 abstract "The interpretation of count data originating from the current generation of DNA sequencing platforms requires special attention. In particular, the per-sample library sizes often vary by orders of magnitude from the same sequencing run, and the counts are overdispersed relative to a simple Poisson model These challenges can be addressed using an appropriate mixture model that simultaneously accounts for library size differences and biological variability. This approach is already well-characterized and implemented for RNA-Seq data in R packages such as edgeR and DESeq. We use statistical theory, extensive simulations, and empirical data to show that variance stabilizing normalization using a mixture model like the negative binomial is appropriate for microbiome count data. In simulations detecting differential abundance, normalization procedures based on a Gamma-Poisson mixture model provided systematic improvement in performance over crude proportions or rarefied counts -- both of which led to a high rate of false positives. In simulations evaluating clustering accuracy, we found that the rarefying procedure discarded samples that were nevertheless accurately clustered by alternative methods, and that the choice of minimum library size threshold was critical in some settings, but with an optimum that is unknown in practice. Techniques that use variance stabilizing transformations by modeling microbiome count data with a mixture distribution, such as those implemented in edgeR and DESeq, substantially improved upon techniques that attempt to normalize by rarefying or crude proportions. Based on these results and well-established statistical theory, we advocate that investigators avoid rarefying altogether. We have provided microbiome-specific extensions to these tools in the R package, phyloseq." @default.
• W2004014148 created "2016-06-24" @default.
• W2004014148 creator A5003674456 @default.
• W2004014148 creator A5050867199 @default.
• W2004014148 date "2014-04-03" @default.
• W2004014148 modified "2023-10-18" @default.
• W2004014148 title "Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible" @default.
• W2004014148 cites W1493454437 @default.
• W2004014148 cites W1564554007 @default.
• W2004014148 cites W1910728686 @default.
• W2004014148 cites W1968105193 @default.
• W2004014148 cites W1969435169 @default.
• W2004014148 cites W1971962952 @default.
• W2004014148 cites W1973628995 @default.
• W2004014148 cites W1989367702 @default.
• W2004014148 cites W1993046026 @default.
• W2004014148 cites W1995393174 @default.
• W2004014148 cites W1999597013 @default.
• W2004014148 cites W2008064453 @default.
• W2004014148 cites W2008985174 @default.
• W2004014148 cites W2017425843 @default.
• W2004014148 cites W2020678906 @default.
• W2004014148 cites W2021129827 @default.
• W2004014148 cites W2026006003 @default.
• W2004014148 cites W2037878492 @default.
• W2004014148 cites W2038838030 @default.
• W2004014148 cites W2055615060 @default.
• W2004014148 cites W2055631148 @default.
• W2004014148 cites W2056279562 @default.
• W2004014148 cites W2058358568 @default.
• W2004014148 cites W2061680337 @default.
• W2004014148 cites W2067564219 @default.
• W2004014148 cites W2068687524 @default.
• W2004014148 cites W2072970694 @default.
• W2004014148 cites W2074414424 @default.
• W2004014148 cites W2080283023 @default.
• W2004014148 cites W2101272820 @default.
• W2004014148 cites W2102921564 @default.
• W2004014148 cites W2107794977 @default.
• W2004014148 cites W2108718991 @default.
• W2004014148 cites W2110065044 @default.
• W2004014148 cites W2114104545 @default.
• W2004014148 cites W2115026474 @default.
• W2004014148 cites W2115057945 @default.
• W2004014148 cites W2118392632 @default.
• W2004014148 cites W2118629634 @default.
• W2004014148 cites W2120778579 @default.
• W2004014148 cites W2121211805 @default.
• W2004014148 cites W2125632841 @default.
• W2004014148 cites W2128599926 @default.
• W2004014148 cites W2133203904 @default.
• W2004014148 cites W2140628770 @default.
• W2004014148 cites W2141425631 @default.
• W2004014148 cites W2142491263 @default.
• W2004014148 cites W2145126338 @default.
• W2004014148 cites W2145664556 @default.
• W2004014148 cites W2147618390 @default.
• W2004014148 cites W2148525391 @default.
• W2004014148 cites W2149756110 @default.
• W2004014148 cites W2152239989 @default.
• W2004014148 cites W2154431984 @default.
• W2004014148 cites W2156631105 @default.
• W2004014148 cites W2156818800 @default.
• W2004014148 cites W2158795865 @default.
• W2004014148 cites W2160187521 @default.
• W2004014148 cites W2160697532 @default.
• W2004014148 cites W2162088497 @default.
• W2004014148 cites W2162767496 @default.
• W2004014148 cites W2170024099 @default.
• W2004014148 cites W2170196186 @default.
• W2004014148 cites W30236741 @default.
• W2004014148 cites W3103302162 @default.
• W2004014148 cites W4230096730 @default.
• W2004014148 doi "https://doi.org/10.1371/journal.pcbi.1003531" @default.
• W2004014148 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/3974642" @default.
• W2004014148 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/24699258" @default.
• W2004014148 hasPublicationYear "2014" @default.
• W2004014148 type Work @default.
• W2004014148 sameAs 2004014148 @default.
• W2004014148 citedByCount "2075" @default.
• W2004014148 countsByYear W20040141482013 @default.
• W2004014148 countsByYear W20040141482014 @default.
• W2004014148 countsByYear W20040141482015 @default.
• W2004014148 countsByYear W20040141482016 @default.
• W2004014148 countsByYear W20040141482017 @default.
• W2004014148 countsByYear W20040141482018 @default.
• W2004014148 countsByYear W20040141482019 @default.
• W2004014148 countsByYear W20040141482020 @default.
• W2004014148 countsByYear W20040141482021 @default.
• W2004014148 countsByYear W20040141482022 @default.
• W2004014148 countsByYear W20040141482023 @default.
• W2004014148 crossrefType "journal-article" @default.
• W2004014148 hasAuthorship W2004014148A5003674456 @default.
• W2004014148 hasAuthorship W2004014148A5050867199 @default.
• W2004014148 hasBestOaLocation W20040141481 @default.
• W2004014148 hasConcept C100906024 @default.
• W2004014148 hasConcept C105795698 @default.
• W2004014148 hasConcept C114289077 @default.

• next