Hi,

You're doing a couple of things wrong. First, prune_samples(samples, x) takes 2 positional arguments, samples and x:

• samples: character of samples to keep or logical, where TRUE, is the samples that you want to keep;

• x: phyloseq-class object.

Therefore, what you're doing wrong:

1. you're giving the arguments in the wrong order, and unless you specific the parameters name, that will never work;

2. you're giving a otu-class object and not a phyloseq class object. Here is important to give a phyloseq-class object, because when you remove samples, it is important to remove these samples not only from the otu table but also from metadata/sample data table - this can only work if you give the phyloseq-class object;

3. sample_names() takes one argument, a phyloseq-class object, you did not give any, so does not work.

To fix and solve all these problems, try the following:

to_remove <- c("Sample1", "Sample5", "Sample10", "Sample30")

z <- prune_samples(!(sample_names(ps) %in% to_remove), ps)

This should work. Assuming that ps is your phyloseq-class object.

I hope this answers your question,

António