Opened 11 years ago

Closed 11 years ago

#507 closed defect (fixed)

'dil' items are created with incorrect value for PoolConc annotation

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: blocker Milestone: Reggie v2.13
Component: net.sf.basedb.reggie Keywords:


There is a bug when calculating concentrations for the extra 'dil' items when pooling libraries. The stored concentration value is the same as the measured 'QubitConc' value from the parent lib and doesn't take into account that the 'dil' item has been diluted in EB. The original quantity should be correct and the actual concentration can be calculated as:

conc(ng/µl) = 5 * quantity(µg) / 1000

The buggy calculations in the code will be fixed as part of #503/#504, but the incorrect values that are already stored in the database need to be fixed using a batch export/import. Instructions should be created as a Trac page and linked from the Reggie download table.

Change History (2)

comment:1 by Nicklas Nordborg, 11 years ago

(In [2027]) References #503: Change pooling strategy

The new implementation works like this:

  1. Use the target volume and target molarity to calculate the amount of each library to take. The resulting value is rounded to one decimal. The result may be higher that the target volume if the concentration is low.
  2. Libraries with high concentration are special cases and are always mixed to 2nM in double the target volume.
  3. Sum up everything and spread out the remaining EB volume equally among all libs. Rounding issues are considered and added to the last lib which may get a higher EB volume.
  4. The selected target volume is stored as an annotation on the pool since the value is needed again when generating the lab protocols.

There is currently not enough checking for extreme cases, eg. if there are many libraries with low concentration the final EB volume may be negative.

NOTE! Since the new implementation is very different from the old, case is needed when installing this update. Pools that have been created with the old Reggie wizard should be completed in the lab and registered before installing this update. Otherwise the lab protocols may show incorrect mixing values.

The incorrect calculations for 'dil' (see #507) items have been fixed.

comment:2 by Nicklas Nordborg, 11 years ago

Resolution: fixed
Status: newclosed

Added instructions for manually fixing issues PoolConc values. See Reggie 2.13 update notes.

Note: See TracTickets for help on using tickets.