Open jiazhou0116 opened 4 years ago
You do not need to make the transformation to compute Bray Curtis, it does it automatically. Susan
On Wed, Jan 1, 2020 at 11:37 AM Jia9 notifications@github.com wrote:
Hi,
Happy new year!
Since the relative abundance is recommended to do beta diversity analysis, I used the following codes to transform our phyloseq object to relative abundance. But when I check taxtab5 (below), I can still only see total abundance. Do you have any ideas on it? Also, the bray-curtis distances of using relative abundance and total abundance are exactly the same. Not sure whether it’s right.
Toad5 is an object that has been removed the otus (counts <=4)
standf = function(x) {x/sum(x)} Toad5.r= transform_sample_counts(Toad5, standf)
taxtab5<-table(tax_table(Toad5.r)[,"Phylum"], exclude = NULL) taxtab5
Thanks,
Jia
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Hi Susan,
Thanks for the quick reply. That's really helpful!
Jia
Susan,
phyloseq::distance converts count data to relative abundances automatically? I wasn't aware. Does vegdist not required a standardization prior to distance calculations? Thanks!
Not for all distances, that just comes from the definition of bray Curtis.
On Tue, Sep 1, 2020 at 1:43 PM kjpaddock notifications@github.com wrote:
Susan,
phyloseq::distance converts count data to relative abundances automatically? I wasn't aware. Does vegdist not required a standardization prior to distance calculations? Thanks!
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-- Susan Holmes John Henry Samter Fellow in Undergraduate Education Professor, Statistics 2017-2018 CASBS Fellow, Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/
Ok thanks!
Hi, could I also ask something about using the relative abundance for beta diversity analysis. I already normalized my OTU data using variance stabilizing transformation using DESEq2. Should I transform my data again into relative abundance for the beta diversity analysis or should I analyze it directly using ordinate function. Thank you so much!
Hi,
Happy new year!
Since the relative abundance is recommended to do beta diversity analysis, I used the following codes to transform our phyloseq object to relative abundance. But when I check taxtab5 (below), I can still only see total abundance. Do you have any ideas on it? Also, the bray-curtis distances of using relative abundance and total abundance are exactly the same. Not sure whether it’s right.
Toad5 is an object that has been removed the otus (counts <=4)
standf = function(x) {x/sum(x)} Toad5.r= transform_sample_counts(Toad5, standf)
taxtab5<-table(tax_table(Toad5.r)[,"Phylum"], exclude = NULL) taxtab5
Thanks,
Jia