Nicklas Nordborg wrote:
>> 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 
> file
> and two raw data files (one matching and one none-matching) how do you tell
> them apart?
I know our lab people is able to trace this somehow, I'll forward the 
> 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?
Wouldn't a percentage make sense here? If more than say 5% of the 
Features in a raw data file does not match the design = bgx file, than 
there is probably an error? This will allow for some changes in the bgx 
file that then wouldn't require the definition of a new array design.

> 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.
Would also be a nice solution.


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