phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
I get an error when I run tax_glom after transforming the data in relative abundance.
data_relative = transform_sample_counts(data, function(x) x / sum(x) )
data_glom <- tax_glom(data_realtive, taxrank ="Phylum",NArm=TRUE)
Error in .local(x, group, reorder) :
as.character(new_names$group) and taxa_names(otu) are not equal:
Lengths (0, 60) differ (string compare on first 0)
If I don't run the transformation, I don't get any error
I get an error when I run tax_glom after transforming the data in relative abundance. data_relative = transform_sample_counts(data, function(x) x / sum(x) ) data_glom <- tax_glom(data_realtive, taxrank ="Phylum",NArm=TRUE)
Error in .local(x, group, reorder) : as.character(new_names$group) and taxa_names(otu) are not equal: Lengths (0, 60) differ (string compare on first 0)
If I don't run the transformation, I don't get any error