Comments (4)
Note that I've also tried the as.matrix() trick offered in another post, but this didn't change the error. I'd really appreciate any insight.
from phyloseq.
Hi @hank00000
Can you try:
relnormps <- phyloseq(otu_table(Relative_Abundance), # data.frame
sample_data(metadata_subset), # data.frame
tax_table(as.matrix(tax_table))) # matrix
from phyloseq.
Hi @hank00000
Can you try:
relnormps <- phyloseq(otu_table(Relative_Abundance, taxa_are_rows = TRUE), # data.frame + sample_data(metadata_subset), # data.frame + tax_table(as.matrix(tax_df))) #matrix
Error in validObject(.Object) : invalid class “phyloseq” object:
Component taxa/OTU names do not match.
Taxa indices are critical to analysis.
Try taxa_names()
Checked and the above TRUEs are still valid.
from phyloseq.
Hi @hank00000 Hmm, that's strange, How about:
# Check taxa names
identical(taxa_names(otu_table(Relative_Abundance, taxa_are_rows = TRUE)),
taxa_names(tax_table(as.matrix(tax_df))))
# Check sample names
identical(sample_names(otu_table(Relative_Abundance,, taxa_are_rows = TRUE)),
sample_names(sample_data(metadata_subset)))
Please use the code block markdown for better visualization out of your output.
For example:
``` r
x <- sum(c(1, 2, 3, 4))
x
```
from phyloseq.
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from phyloseq.