Merging metadata with otu table in a phyloseq object

[lynneitelson]

Hi!

when i make a phyloseq object like this:

``ps2 <- phyloseq(otu_table(seqtab, taxa_are_rows=FALSE), tax_table(taxa1))"

It works just fine and by using "sample_names" i see that the names are 1,2,3,4,mock,ng

When i add my metadata the following error occurrs:

``ps2 <- phyloseq(sample_data(metadata),otu_table(seqtab, taxa_are_rows=FALSE), tax_table(taxa1))"

The sa metadata_ps.csv The sample names of the original phyloseq object and the metadata are the same so i can't seem to figure out the problem.

metadata_ps.csv

Thankyou,

Lynne

[gmteunisse]

Hi Lynne, some general things you can check are:

• Are the samples in the same order in the otu_table and the sample_data, or are there any samples in one table that are not in the other? Check this using all(row.names(metadata) == row.names(seqtab)).
• I notice you use integers as sample names, but R doesn't like columns to start with an integer, and therefore prepends an X (or V) to columns with those names. Have you check whether this is the case?
• Naively reading in the provided metadata file will not set the row.names; rather, it will create a column named X that contains that information. Have you made sure that the first column is taken to be the row.names?

If you want more tailored advice, I recommend you to also upload a partial otu_table and tax_table, so we can see where the problem might occur.