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Reply to: "A fair comparison"

Nature Methods volume 11, pages 359–360 (2014)Cite this article

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Paulson et al. reply:

Costea et al.1 challenge the fairness of the results presented in the first figure of our paper2, which explored the effect of normalization and transformation procedures on clustering analysis of marker-gene survey data (for example, 16S metagenomics data). Specifically, they argue that the “conceptually simpler” total-sum scaling (TSS) normalization method should not be dismissed by unfair characterization of its performance. In our figure, log transformation was applied to data normalized with our cumulative-sum scaling (CSS) method but not to TSS-normalized data. However, we stated clearly in the Online Methods section that CSS-normalized data were log transformed, and we showed the performance of log-transformed TSS-normalized data as Supplementary Figure 2 in our paper2.

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Figure 1: Effect of pseudocount choice on total-sum scaling (TSS) normalization.

References

  1. Costea, P.I., Zeller, G., Sunagawa, S. & Bork, P. Nat. Methods 11, 359 (2014).

    Article  CAS  Google Scholar 

  2. Paulson, J.N., Stine, O.C., Bravo, H.C. & Pop, M. Nat. Methods 10, 1200–1202 (2013).

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  1. mpop@umiacs.umd.edu

Authors and Affiliations

  1. Graduate program in Applied Mathematics, Statistics, and Scientific Computation, University of Maryland, College Park, Maryland, USA

    Joseph N Paulson

  2. Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA

    Joseph N Paulson, Héctor Corrada Bravo & Mihai Pop

  3. Department of Computer Science, University of Maryland, College Park, Maryland, USA

    Héctor Corrada Bravo & Mihai Pop

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  1. Joseph N Paulson
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  2. Héctor Corrada Bravo
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  3. Mihai Pop
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Correspondence to Héctor Corrada Bravo or Mihai Pop.

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Paulson, J., Bravo, H. & Pop, M. Reply to: "A fair comparison". Nat Methods 11, 359–360 (2014). https://doi.org/10.1038/nmeth.2898

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