Hi!
I’m new to this package, and I’m wondering how do I encode the blanks or negative controls in the metadata that I’m supplying to maaslin.
Currently, I have a column called Condition, where 0s are the samples, and 1 are the controls.
Should I remove the pathways which have been seen in the negative controls based on some filter, or does maaslin handle this automatically?
Hi,
If you mean blanks/negative controls in the sense that you had a swab with nothing on it and sequenced it, I’d check the sequencing and taxonomic assignment results to make sure you’re not seeing much on it (since that would indicate contamination), but then I’d just exclude those downstream.
If by negative controls you mean whichever group of samples wasn’t given the treatment, you’d just include the column of control vs. treatment as your fixed effect.
Will