Hi all,
Since this is my first post in this list: Hello to everyone reading!
In order to use ecological count data in ordination methods like
Principal Component Analysis (PCA) or Redundancy Analysis (RDA), they
have to be transformed. Ecologists [1,2] proposed a number of useful
transformations for count data, such as chi-square or Hellinger
transformation, which are also available in the decostand function of
the vegan package.
With the advent of high-throughput sequencing, ordination methods have
been applied to metagenomic sequence counts (namely of 16S rDNA
amplicons). I have been using Hellinger transformation with such data in
combination with RDA for quite a while with satisfactory results.
In the past years, new normalization techniques specifically suited for
metagenomic count data, namely cumulative-sum scaling (CSS) [3] were
developed. The authors claim that their CSS method is superior to
traditional total-sum scaling (TSS). TSS is also the first step in
Hellinger transformation (followed by taking the square root).
I am thus wondering if I should switch to CSS transformation of
amplicon counts for use in RDA - probably in combination with
square-root transformation to lessen the impact of highly abundant taxa.
Any experience with this matter or suggestions from your side?
Thanks in advance for sharing your thoughts with me!
References:
1. Legendre P, Gallagher ED. 2001. Ecologically meaningful
transformations for ordination of species data. Oecologia 129:271-280.
2. Borcard D, Gillet F, Legendre P. 2011. Numerical ecology with R.
Springer, New York.
3. Paulson JN, Stine OC, Bravo HC, Pop M. 2013. Differential abundance
analysis for microbial marker-gene surveys. Nat Methods 10:1200-1202.
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