Hello BASErs,

After little hands-on session with BASE I have reported some 
bugs/comments on trac:


These are rather minor things, but there is something that worries us 
more. I know that the array design concept is not really holding when 
comes to Illumina technology. It is more like a list of features. I am 
also aware of that some features are being removed from consecutive 
versions of .bgx files. Thus the 'skip feature' option had to be 
introduced to import plugin allowing skipping some features that are 
present in raw data files, but not .bgx files. It is a common practice 
to run this plugin with skip option set to true.

This has a serious implication: one can accidentally import data from 
human IBS file to a raw bioassay that has a mouse (for example) array 
design attached to it. If features are allowed to be skipped, a common 
subset of features will be imported to db and no warnings will be issued 
about wrong design. To mislead the user even more, the raw data file 
will be marked as validated (because plugin finished run with no errors).

The array design concept was intended to provide a way of checking if 
the right raw data files are linked with right samples/extracts in the 
experiment, and that the right data is analyzed in experiment. It seems 
that it might not be the case for Illumina.

Do you think there is a way to improve this and provide control over 
what gets imported with what design?

Best wishes,

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