Dear Jari,
first of all, thank you so much for creating and sustaining this amazing ressource and workflow. After a course on multivariate statistics, based on vegan, I finally was able to apply it to my amplicon sequencing data.
On a data set on phylum level, dealing with 47 taxa, everything went fine. Now I wanted to perform several ordinations etc. on the ASV (species) level, but here, 25000 taxa or species seem to create issues for R. Is there a maximum number of species possible with vegan in R?
The source of error is that uploading my tsv as.dataframe.list this time supplies a large list instead of X observations on Y sites. Do you know how this could be solved?
Code:
#Loading my response data: 16S amplicons counts (~phylum abundances = 48 variables) in 10 different sites over 2 year (=18 sites/observations)
ampli <- as.data.frame.list(read_tsv("16S_ASV.txt"))
ampli.t<- t(ampli) #because of the huge number I couldn't transpose it in Excel
ampli.2 <- ampli.t[-2,]
colnames(ampli.2) <- ampli.t[1,]
ampli<- (ampli.2[-1,])
While this worked for a smaller dataset, it did not for this larger one.
Smaller data set (did not need to be transposed, but worked):
ampli <- as.data.frame.list(read_tsv("16S_phylum.txt"))
ampli.2 <- ampli[,-1]
rownames(ampli.2) <- ampli[,1]
ampli<- ampli.2
Dear Jari,
first of all, thank you so much for creating and sustaining this amazing ressource and workflow. After a course on multivariate statistics, based on vegan, I finally was able to apply it to my amplicon sequencing data.
On a data set on phylum level, dealing with 47 taxa, everything went fine. Now I wanted to perform several ordinations etc. on the ASV (species) level, but here, 25000 taxa or species seem to create issues for R. Is there a maximum number of species possible with vegan in R?
The source of error is that uploading my tsv as.dataframe.list this time supplies a large list instead of X observations on Y sites. Do you know how this could be solved?
Code:
#Loading my response data: 16S amplicons counts (~phylum abundances = 48 variables) in 10 different sites over 2 year (=18 sites/observations)
ampli <- as.data.frame.list(read_tsv("16S_ASV.txt"))
ampli.t<- t(ampli) #because of the huge number I couldn't transpose it in Excel
ampli.2 <- ampli.t[-2,]
colnames(ampli.2) <- ampli.t[1,]
ampli<- (ampli.2[-1,])
While this worked for a smaller dataset, it did not for this larger one.
Smaller data set (did not need to be transposed, but worked):
ampli <- as.data.frame.list(read_tsv("16S_phylum.txt"))
ampli.2 <- ampli[,-1]
rownames(ampli.2) <- ampli[,1]
ampli<- ampli.2