#1426 closed defect (fixed)

Warn/fix unreasonble values for RNA remaining quantity in JSON files

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.41.1
Component: net.sf.basedb.reggie Keywords:


The JSON files that are imported by the "Import externally processed samples" wizard seem to have unreasonable value for the original and remaining quantity. It seems like only a few nanograms have been used in the library prep. The higher the concentration it seems like a lot less has been used. The values makes more sense if the difference between original and remaining quantity is interpreted as a volume (in µl).

Example, in the JSON we have:

  • Original quantity (ng): 23980
  • Remaining quantity (ng): 23978
  • Concentration (ng/ul): 436

It is not reasonable that only 2ng was used, but 2µl*436ng/µl=872ng is more likely (though rounding the quantities to whole numbers probably affect the result).

The import wizard should check the original and remaining quantity and issue a warning if the difference is less than 100ng. It should also try to re-calculate the quantities based on the assumption that the difference is a volume in µl and if it makes more sense use that when importing instead.

Change History (2)

comment:1 by Nicklas Nordborg, 20 months ago

In 6943:

References #1426: Warn/fix unreasonble values for RNA remaining quantity in JSON files

Implemented a check and fix for the "used quantity".

comment:2 by Nicklas Nordborg, 20 months ago

Resolution: fixed
Status: newclosed
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