QIIME2 view of regression summary empty CSV

Hi there :slight_smile:

I'm interested in looking at a CSV table of the FDR corrected p-values after a gneiss regression summary (see files). I assume that the FDR values are likely more reliable than the un-corrected p-values?

Anyway, I am having troubles retrieving this information from the qvz file. I see on the heatmap, that many of the balances have coefficients and pvalues, however the file is empty when I download it. Could this be a bug, or does this mean that there are no p-values (i.e., the data is terrible :P).


I'm using 2018.8.

qiime gneiss correlation-clustering \
     --i-table $input_table \
     --o-clustering hierarchy.qza
qiime gneiss ilr-hierarchical \
     --i-table $input_table \
     --i-tree hierarchy.qza \
     --o-balances balances.qza
qiime gneiss ols-regression \
      --p-formula "Sample_type" \
      --i-table balances.qza \
      --i-tree hierarchy.qza \
      --m-metadata-file $metadatapath \
      --o-visualization regression_summary_Sample_type.qzv

input_table -- filtered for more than 10 reads per feature across the samples
table.0.97.with-unassigned.0.7.frequencycutoff.10.RA1.qza (39.3 KB)

sample_info_all5.txt (5.0 KB)

CSV file downloaded from QIIME2view
fdr-corrected-pvalues (2).csv (3.3 KB)

Regression summary
regression_summary_Sample_type.qzv (180.7 KB)

I think I managed to solve this issue!

The data I was analyzing was a subset of the total samples read-in with the metadata. First, I had filtered my feature table and sequences to include only the sequences of interest. I then used these files to do the gneiss analysis (build hierarchies and balances). However, the ols-regression requires a metadata file.
My metadata file had all the samples from my sequencing run and therefore the other metadata components were being included in the model (i think??). If I use a filtered metadatafile with only the samples I was looking to compare, I managed to get normal CSV files.

Does this make sense?



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