q2-longitudinal differences

User Support
1

I have been working with this for hours after watching the ECAM video

I worked with the ecam Shannon.qza and everything went fine but while working with my sample I keep getting this error with all my Alpha diversity and ordinary distance was returning no values at my State 1 and State 2

qiime longitudinal pairwise-differences
--m-metadata-file Protein_metadata.tsv
--m-metadata-file core-metrics-results/shannon_vector.qza
--p-metric shannon
--p-group-column delivery
--p-state-column month
--p-state-1 0
--p-state-2 12
--p-individual-id-column studyid
--p-replicate-handling random
--o-visualization pairwise-differences.qzv
Plugin error from longitudinal:

metric must be a valid metadata or feature table column.

Debug info has been saved to /var/folders/nq/42xk0g_945110bzykmkwd2980000gq/T/qiime2-q2cli-err-99k5z13z.log

I later changed the shannon to Shannon_entropy as advised in one of previous posts in this forum, that ran but it's not returning any value

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2

Welcome to the forum!
Based on the screenshots you shared, the issue is that you don't have data for the same subject in both states. In other words, you should have, for example, Subject1 sampled both at state 1 and state 2, the same for Subject2 and so on. If you have data from Subject1 only for state 1, and from Subject2 only for state 2, you will get warnings like in the screenshot.

Best,

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3

Thank you for this

My plan is to see how shannon changes from day 0 to day 28 and not just day 0 and day 28

I used volatility after this your explanation and it gave me what I wanted

4

The follow-up to my question is how do I generate relative taxa table from my feature table?
qiime longitudinal nmit
--i-table Protein_table.qza
--m-metadata-file Protein_metadata.tsv
--p-individual-id-column studyid
--p-corr-method pearson
--o-distance-matrix nmit-dm.qza

Error

(1/1) Invalid value for '--i-table': Expected an artifact of at least type
FeatureTable[RelativeFrequency]. An artifact of type FeatureTable[Frequency]
was provided.

5

I first converted my FeatureTable[Frequency] to FeatureTable[Relative frequency]
qiime feature-table relative-frequency
--i-table Protein_table.qza
--o-relative-frequency-table feature-table/relative.table.genus.qza

I then generated distance matrix .qza
qiime longitudinal nmit
--i-table feature-table/relative.table.genus.qza
--m-metadata-file Protein_metadata.tsv
--p-individual-id-column studyid
--p-corr-method pearson
--o-distance-matrix nmit-dm.qza
Saved DistanceMatrix to: nmit-dm.qza

However, at the final point I got this error from

qiime diversity beta-group-significance
--i-distance-matrix nmit-dm.qza
--m-metadata-file Protein_metadata.tsv
--m-metadata-column Diet
--o-visualization nmit.qzv
Plugin error from diversity:

All values in the grouping vector are unique. This method cannot operate on a grouping vector with only unique values (e.g., there are no 'within' distances because each group of objects contains only a single object).

Debug info has been saved to /var/folders/nq/42xk0g_945110bzykmkwd2980000gq/T/qiime2-q2cli-err-ymeu51h9.log

What do I do?

7

Here is the core error:

This is a stat test that's comparing groups based on the --m-metadata-column Diet, but there is only one Diet! Because every Diet is set to ARD there is no other group to compare the ARD diet to...

Perhaps there are more samples or add or something is wrong with that metadata file? Getting in touch with the ECAM team may help answer these questions.

On a more personal note, you are making very good progress with Qiime2. Good job converting the table to Relative frequency!

Let us know if you have more questions!

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