Hi, To add to Vegard point about quality assessment, there are various packages in R to perform QC on CEL files. Reports generated as png or pdf would be nicely stored at RawBioassay level (ideally) or at Experiment level (if nothing else is available).
One a related issue, I think there is already a ticket to create an new Annotation Type which type could be set to 'File' allowing BASE2 to cope with imaging data attached to Source or Samples as well as QC reports for individual RawBioAssays. Then a question: Would the redesign remove the current requirement for users to set a unique platform when creating a new experiment ? I have 2 use cases in mind: 1. I am performing a microarray experiment where the same samples are assayed for both gene expression on affymetrix and methylation status using a custom made array 2. I am running first a whole transcriptome scan on agilent arrays and then running confirmation tests on focused PCR arrays such as ABI SuperArrays one my top 100 most differentially expressed genes as identified following whole transcriptome scan. (I am still looking for information regarding the output generated from PCR arrays) cheers Philippe vegard nygaard wrote: > Hi. I have a proposal. > > >> Are there other item types that may need files? >> http://base.thep.lu.se/ticket/721. .. >> > > I have sometimes heard the need to store quality control reports for > extracts and labeled extracts. A lab tool called BioAnalyzer makes a file > with a plot to better assess the quality (purity) of your rna or dna. > Another tool called nanodrop does something similar also for labeled > extract. I don't think these files should be parsed in any way, just stored > with a link to their item on an appropriate page. > > This is not a critical thing, but nice to include. > > Vegard. > > >> -----Original Message----- >> From: [EMAIL PROTECTED] [mailto:basedb-devel- >> [EMAIL PROTECTED] On Behalf Of Nicklas Nordborg >> Sent: Friday, September 21, 2007 8:11 AM >> To: BASE dev >> Subject: [basedb-devel] Comments wanted about new feature in BASE 2.5: >> Store data in files instead of in the database >> >> Hello all, >> >> We are currently working on the issue of keeping data (ie. raw data, >> array design data and possible analyzed data) in files instead of >> importing it into the database. It is alread possible to do that for >> Affymetrix experiments, but the solution can't be used to give the same >> functionality for other platforms. >> >> We have put together a few draft documents describing a possible design >> (database, API, etc...) to solve this issue in a more general way. In >> practice, it will be possible to let BASE store data for any platform. >> Using/analyzing the data will be a plug-in issue to 100% and is no >> longer a concern for the BASE core. >> >> So, anybody that is interested in checking this out can go to >> http://base.thep.lu.se/ticket/721. There are links to relevant >> documentation. If you have any comments or other ideas, please let us >> know. One thing we need help with is the list of pre-installed >> platforms. Anybody with knowledge of different platforms and what types >> of files they generate please tell us and we will try to add as much as >> possible to the standard BASE distribution. >> >> Prototype development has already started. We expect the design to be >> more or less finalized in a few weeks. Minor details may still be >> changed after that. >> >> /Nicklas >> >> ------------------------------------------------------------------------- >> This SF.net email is sponsored by: Microsoft >> Defy all challenges. Microsoft(R) Visual Studio 2005. >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >> _______________________________________________ >> basedb-devel mailing list >> basedb-devel@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/basedb-devel >> > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2005. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > basedb-devel mailing list > basedb-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/basedb-devel > -- **************************************************************** Philippe Rocca-Serra (Ph.D) NET Project - Technical Coordinator http://www.ebi.ac.uk/net-project EBI- The European Bioinformatics Institute EMBL Outstation Hinxton Wellcome Trust Genome Campus CB10 1SD Cambridge, UK email: [EMAIL PROTECTED] Tel: +44 (0) 1223 492 553 Fax: +44 (0) 1223 494 468 European Nutrigenomics Organization http://www.nugo.org **************************************************************** ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
