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Description
mp_term assigned for "Not significant" classification_tag which leads to incorrect display on the website.
- Page with a bug:
https://www.mousephenotype.org/data/supporting-data?mgiGeneAccessionId=MGI:2150037&mpTermId=MP:0004647
Two significant p-values are shown. However, when we scroll down, the classification is "Not significant," and there is no p-value displayed. The Statistical Method tab also shows N/A values.
- Solr query for the data from the page:
https://www.ebi.ac.uk/mi/impc/solr/statistical-result/select?q=colony_id:EPD0002_2_B07%20AND%20parameter_name:%22Number%20of%20lumbar%20vertebrae%22
- Both datasets have the same p-value on the website as in the Solr core.
- The
classification_tagis "Not significant" in the Solr core as we see on the website. - The
mp_termwas assigned by the annotation pipeline, which means that these p-values were considered significant. Otherwise, themp_termwouldn't have been assigned.
classification_tagis generated by OpenStats R package.
mainAgeing function runs VectorOutput0 function that use classificationTag function from OpenStats:
Line 2186 in 2ab335e
| p1$`Classification tag` = OpenStats:::classificationTag(c.ww0$NormalObj) |
Website use classification_tag field from statpacket to generate pages. Issue appears in the statistical pipeline.
- Search for
classification_tag:"Not significant" ANDsignificant:true.
Five data points for legacyEuroPhenomewere found:
https://www.ebi.ac.uk/mi/impc/solr/statistical-result/select?fl=classification_tag,significant,resource_name,parameter_stable_id&q=classification_tag:%22Not%20significant%22%20AND%20significant:true
To debug this as a first step we need to investigate classificationTag function from OpenStats.
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