Hard coding in DiffBind DBA.R line 968
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Ou, Jianhong ★ 1.2k
@ou-jianhong-4539
Last seen 26 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?

Jianhong.

DiffBind • 132 views
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Rory Stark ★ 4.0k
@rory-stark-5741
Last seen 5 days 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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