Pairwise differences acording to taxonomy

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1

Hello!

i'm trying to do pairwise analysis in order to find taxonomy changes between 2 time points.
first of all I have changed my feature table to relative frequency:

qiime feature-table relative-frequency --i-table table.qza --o-relative-frequency-table table_relative-frequency.qza

and then used the output here:

qiime longitudinal pairwise-differences --m-metadata-file mapping_file.tsv --m-metadata-file table_relative-frequency.qza --p-metric featuretable --p-group-column Mucositis_Grade_Range1 --p-state-column Day_Group --p-state-1 _min1 --p-state-2 7_13 --p-individual-id-column Personal_ID --p-replicate-handling random --o-visualization pairwise-differences.qzv

I got an error:

There was an issue with viewing the artifact mucositis_merged-samples_readyforanalysis_relative-frequency_140818.qza as QIIME 2 Metadata:

Artifact <artifact: FeatureTable[RelativeFrequency] uuid: 37d09292-dbe8-4db9-8e26-40e599957475> cannot be viewed as QIIME 2 Metadata.

I don't know what i'm missing :-\

Thanks!

3

here is your problem! Feature tables should be input as table not a metadata-file. So the following command should work:

qiime longitudinal pairwise-differences \
    --i-table table_relative-frequency.qza \
    --m-metadata-file mapping_file.tsv \
    --p-metric featuretable \
    --p-group-column Mucositis_Grade_Range1 \
    --p-state-column Day_Group \
    --p-state-1 _min1 \
    --p-state-2 7_13 \
    --p-individual-id-column Personal_ID \
    --p-replicate-handling random \
    --o-visualization pairwise-differences.qzv

I hope that helps!

5

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