alpha-group significance metadata requiring categorical data

But all the samples are in Capitals? I did however rewrite them all again and found that sample11 was written incorrect in the manifest and have to corrected this, validated and continued with the tutorials. my next error lol again with the metadata. I could’nt run alpha diversity as there was no categorical data, yet Sample ID is categorical - I have 15 samples that corresponding to two groups. Do these groups need to be added into the metadata in order to become the categorical data?
qiime diversity alpha-group-significance \

–i-alpha-diversity core-metrics-results/faith_pd_vector.qza
–m-metadata-file metadata.tsv
–o-visualization core-metrics-results/faith-pd-group-significance.qzv
Plugin error from diversity:

Metadata does not contain any columns that satisfy this visualizer’s requirements. There must be at least one metadata column that contains categorical data, isn’t empty, doesn’t consist of unique values, and doesn’t consist of exactly one value.

Debug info has been saved to /tmp/qiime2-q2cli-err-nj5c8xco.log
(qiime2-2019.10) [email protected]:~/Raw_data/Workingdata$
(qiime2-2019.10) [email protected]:~/Raw_data/Workingdata$ qiime diversity alpha-group-significance \

–i-alpha-diversity core-metrics-results/evenness_vector.qza
–m-metadata-file metadata.tsv
–o-visualization core-metrics-results/evenness-group-significance.qzv
Plugin error from diversity:

Metadata does not contain any columns that satisfy this visualizer’s requirements. There must be at least one metadata column that contains categorical data, isn’t empty, doesn’t consist of unique values, and doesn’t consist of exactly one value.

Debug info has been saved to /tmp/qiime2-q2cli-err-tszuojwj.log

Hi @Rsimmonds,
I moved this to a new thread as it was no longer related to the original issue raised.
Glad the initial metadata error was resolved.

Yes! Otherwise, how would the test know which groups these samples belong to to compare them, right?

The error is explaining exactly that as well, simply add a new column to your metadata file which has the sample’s memberships (groupings) and rerun the test.
Good luck!

Thankyou. I added two new columns and rerun all the Data. When visualising it I can now see categories (my 15 samples) is there any way to merge 1-6 into 1 group?

Hi @Rsimmonds,
Great! If the new columns you added have sample designations, for example:

| sample-id | group     | age   |
|-----------|-----------|-------|
| S1        | healthy   | child |
| S2        | healthy   | child |
| S3        | healthy   | adult |
| S4        | treatment | adult |
| S5        | treatment | teen  |
| S6        | treatment | teen  |

Then alph-agroup significance will run a Kruskal-Wallis test using your new columns as grouping maps. So you will see boxplots comparing health vs treatment samples, and if you use the drop-down menu from the top of the plot, you can select the other group say age, and then you’ll see boxplots comparing the 3 age categories.

2 Likes

Perfect thankyou
I attended the qiime course a few weeks ago in Washington and although I know what I want to do, I’m having trouble doing it.

4 Likes

No problem @Rsimmonds,
It takes a while to get familiar with everything but it does get easier!
Were you able to get what wanted here?

Let us know if you run into any other issues, we’re always happy to help.

2 Likes