Renaud Gaujoux wrote: > Hi, > > thanks for your reply. It worked perfectly adding the File type. > My questions are then: > - why do I need to give the file type when the extension 'cel' is > defined in the Data file types and related to the type 'CEL file' (I've > tried with the files' extensions in lower case also but did not work)? > - same question with Platform, when I give the array design (which > requires a valid Platform at creation)?
Almost everything in BASE is loosely connected and many things are optional. Platform is not optional, but array design is, so unless you want the "generic" platform the file should contain a "platform" column. Trying to guess what is related will probably only confuse users more, so we try to stick to something that works in the same way in all cases. Not all cases are like the Affymetrix case with specific file extensions. A lot of data files comes as .csv or .txt. > My objective here is to setup BASE so that the task are highly > automated, as I think it's got this capability. For example, I think > even the Array Design could be discovered from the CEL files, as from > what I've seen the headers contain a string that identify the chip > (HG-U133_Plus_2.1sq, Mouse430A_2.1sq, ...). Is there some development in > that way? No. It is a special case that will only work with Affymetrix. > I'm a programmer but not very comfortable with Java and would rather use > standard plugins from the BASE-team to achieve that. We are not planning any more specific Affymetrix support right now. In fact, a lot of Affymetrix things (eg. information about file formats, etc.) in BASE has been contributed by external users. Our goal is to keep the core plug-ins as generic as possible and they should work with any platform without special cases. It is certainly possible to make other plug-ins that are more streamlined for the Affymetrix platform, but I feel that is a thing that has to be contributed by others that actually use Affymetrix regularly. > Concerning Illumina data, what about adding the nuID used by > Bioconductor relevant annotation packages as probe identifier? It find > it is a clean and simple way to prevent confusion of probe id > discrepancy between different verisons of Illumina annotations. What is nuID? I can't find anything that seems related to this in the example Illumina data files we have. If you have files that contains nuID you can choose to have that as identifier if you want to. As long as you are consistently using the same identifier BASE doesn't care about what you are using. /Nicklas ------------------------------------------------------------------------------ This SF.net email is sponsored by: High Quality Requirements in a Collaborative Environment. Download a free trial of Rational Requirements Composer Now! http://p.sf.net/sfu/www-ibm-com _______________________________________________ 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
