Thank you!
Nicklas Nordborg wrote:
I have added two tickets. One is for the Bead summary importer in the
Illumina package: http://baseplugins.thep.lu.se/ticket/240
The other is for the Overview functionality in the BASE web client:
http://base.thep.lu.se/ticket/1362
We'll probably be able to fix #1362 this week and before BASE 2.13 is
released. Don't know when the next Illumina package (1.4) will be released
though since there are some other issues that are not yet complete.
/Nicklas
Kjell Petersen wrote:
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
question.
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.
best,
Kjell
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