tyring to subset phyloseq object - error sample data must have no zero dimensions about qiime2r HOT 4 CLOSED

Believe it or not, I do not use phyloseq directly very often but I can try to help. I think the error is suggesting after applying the filter there are no samples. If you look at sample_data(physeq1) is there a column called country and does it have "Namibia" for at least one sample?

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Hi @jbisanz,

Thanks for your reply. I had a look at the sample data and it looks like Namibia is there. My table looks a bit weird tho, it is a .txt file so not sure if this is the problem, it worked fine in qiime2 though.

head(sample_data(physeq1))
Sample Data: [6 samples by 5 sample variables]:
snail.id country site morph.id.genus
020221-AT-1 N.1A.Lym1.5 Namibia 1A Lymnaea/Radix
020221-AT-10 N.1D.Bul1.3 Namibia 1D Bulinus
020221-AT-100 SA.1Db.Biom.un South Africa 1D Biomphlaria
020221-AT-101 SA.1D.Bmp.1 South Africa 1D Biomphlaria
020221-AT-102 SA.5A.Bmp.1 South Africa 5A Biomphlaria
020221-AT-103 SA.5A.Bmp.2 South Africa 5A Biomphlaria
shedding
020221-AT-1 no
020221-AT-10 no
020221-AT-100 no
020221-AT-101 no
020221-AT-102 no
020221-AT-103 no

Thanks, Anya

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Hi @jbisanz I had a look at my data and noticed that "Namibia" was actually "Namibia ". Adding the space into my code fixed the problem!

Best
Anya

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Great to hear!

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