Pawel Sztromwasser wrote:
> Hello BASErs,
> After little hands-on session with BASE I have reported some 
> bugs/comments on trac:

Great. We'll have a look at them.

> 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?

One problem is that the raw data files contains no information whatsoever about
which array design that was used. Do you have any ideas yourself? Given a BGX 
and two raw data files (one matching and one none-matching) how do you tell
them apart?

The only thing I can think of is to report an error if the number of skipped
data lines goes above a certain threshold. Any idea about what a good value
for that threshold might be? 10? 100?

Another possibility is to add a check in the experiment overview that compare
the number of features on the array design with the number of raw data spots in
the raw bioassay. If the difference is too big a warning could be generated.


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