Hard coding in DiffBind DBA.R line 968
Entering edit mode
Ou, Jianhong ★ 1.2k
Last seen 9 days ago
United States

Hi Rory and Gord,

A student report a potential bug in DiffBind3. At DBA.R line 967-968,

pv.DBA(DBA, method,bTagwise=bTagwise,
           minMembers=3, bParallel=bParallel)

will it be better to be replaced by

pv.DBA(DBA, method,bTagwise=bTagwise,
           minMembers=minMembers, bParallel=bParallel) # minMembers = parameter from pv.contrast

or keep minMembers parameter?


DiffBind • 104 views
Entering edit mode
Rory Stark ★ 3.9k
Last seen 1 day ago
CRUK, Cambridge, UK

Thank you for noticing and reporting this potential issue relating to the minimum number of sample replicates required to form a contrast.

In this case, the code is correct, as the line appears in dba.analyze(), which does not take minMembers as a parameter. If this function is called on an object with no established contrasts, the defined behavior is to set up the default contrasts (with the default being minMembers=3). If a user needs to automatically establish contrasts using a different value for minMembers, they should call dba.contrast() explicitly, providing the desired value for minMembers, prior to calling dba.analyze().


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