mothur

Error in nmds plots with unifrac files

#1

Hi,

I have generated weighted and unweighted unifrac distances on mother v 1.41.1 Nov 2018 edition. These were generated fine, however when I come to generate nmds axis for both the weighted and unweighted unifrac distances, I get the following message:

mothur > nmds(phylip=final.otu.table.braycurtis.1.lt.tre1.weighted)

[ERROR]: expected a number and got Baseline-Baseline_DietScore. I suspect you entered a column formatted file as a phylip file, quitting.
logout
Saving session…
…copying shared history…
…saving history…truncating history files…
…completed.
Deleting expired sessions…13 completed.

[Process completed]

my unifrac distance files were generated using the following command:
unifrac.unweighted(tree=final.otu.table.braycurtis.1.lt.tre, group=xxx.design, random=T)

I have tried adding “distance=lt” into the unifrac.weighted command to produce a phylip distance matrix however the distance matrix generated groups my samples into their treatment groups so the nmds command only generates nmds axis for the groups and not individual samples.

I have had no issues with the nmds command in previous experiences working with datasets containing only two treatment groups, however the current dataset is with 11 treatment groups and 19 feed & water samples.

Any help would be greatly appreciated

Chris

closed #2

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#3

unifrac.unweighted(tree=final.otu.table.braycurtis.1.lt.tre, group=xxx.design, random=T)

I am assuming the tree file relates your samples, and the group file assigns your samples to their treatment groups. If so, the unifrac results will be for the treatment comparisons. To compare the samples, you want a tree that relates your sequences and a group file that maps the sequence names to their samples.

Alternatively, you could use the dist.shared command to generate distances between the samples and then run the nmds command. You can see how we run this part of the analysis in Pat’s example, https://www.mothur.org/wiki/MiSeq_SOP#OTU-based_analysis.