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 > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > basedb-users-requ...@lists.sourceforge.net ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
