Maaslin3 error message

Downstream analysis and statistics
1

Hello again,

I am trying to process relative abundance species data which is already TSS normalised, so I selected normalisation = NONE. However, I am getting an error message ‘Error in d[setdiff(unique(metadata[, names(l)]), names(d))] ← NA :
only 0’s may be mixed with negative subscripts’.
When I look in the features folder all of the zeros in my data are converted to N/A. Do you know what is happening here, and how I might work around it?
Many thanks,
Katherine

2

Hi Katherine,

I’m not sure what’s going on without looking at the log file or a small reproducible example. However, you might check that your inputs are being read as numerics rather than e.g. characters, and if you just turn on TSS it shouldn’t change anything for data that are already TSS.

Will