About using relative abundance for beta diversity

[jiazhou0116]

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

[spholmes]

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 ***@***.***> 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 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1288?email_source=notifications&email_token=AAJFZPMYXPI5PITQTO62TPTQ3TWHJA5CNFSM4KB4ON62YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IDSX5JQ>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJFZPLF6YQUNKSUYTEWURDQ3TWHJANCNFSM4KB4ON6Q> .

-- 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/

[jiazhou0116]

Hi Susan,

Thanks for the quick reply. That's really helpful!

Jia

[kjpaddock]

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!

[spholmes]

Not for all distances, that just comes from the definition of bray Curtis.

On Tue, Sep 1, 2020 at 1:43 PM kjpaddock ***@***.***> 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! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1288 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJFZPPOYKSO65GWZPGBLPTSDVMHBANCNFSM4KB4ON6Q> . --

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/

[kjpaddock]

Ok thanks!

[tcrispino13]

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!