Phyloseq taxa don't match error, but TRUE when asked if values match?

[hank00000]

I originally pulled the OTU table from a phyloseq object and modified it with a normalization method not supported within the package. Now I want to re-create a phyloseq object but am running into issues.

I've created a normalized and relative abundance table and made the row names the OTU sequences, and the column names sampleIDs. I also have a taxa table with row names as OTU sequences, and the tax info as columns. My metadata has rownames as sampleID and the variables as columns.

I get the following affirmations :

rownames(Relative_Abundance) == rownames(tax_table)
[1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[20] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[39] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[58] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[77] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[96] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[115] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[134] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[153] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[172] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[191] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[210] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[229] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[248] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[267] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[286] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[305] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[324] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE

rownames(metadata_subset) == colnames (Relative_Abundance)
[1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[20] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[39] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[58] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[77] TRUE TRUE TRUE TRUE TRUE

relnormps <- phyloseq(otu_table(Relative_Abundance),
sample_data(metadata_subset),
tax_table(tax_table))

Error in validObject(.Object) : invalid class “phyloseq” object:
Component taxa/OTU names do not match.
Taxa indices are critical to analysis.
Try taxa_names()

Any suggestions? Much appreciated.

[hank00000]

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.

[ycl6]

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

[hank00000]

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.

[ycl6]

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
```