vegard nygaard wrote: > Hi. I am searching for some information in BASE2 that I often looked at in > BASE1. I can't find it. Can you help me? This is not a migration question. > The BASE2 data is fresh test data. > > I have a Raw bioassay and want to see what raw data file I used to create > it. I can't trace that info anywhere in the BASE2 GUI or in the API. Where > is that information hidden?
This information is not stored (*). For BASE 2.5 we are working on a generic solution for attaching files to various items (raw bioassays, array designs, etc), and also an option to keep the data in the files instead of importing it into the database. This is how it currently works for Affymetrix data, but the solution can't be extended to cover other formats. For more info see http://base.thep.lu.se/ticket/721. > And what happens to the raw data file when it is used to make a raw > bioassay. In BASE1 I think it was automatically copied to another place and > you could actually delete it from upload, but it would still be there > accessible from the raw bioassay page. The downside of this was a lot of > double storage. How is this handled in BASE2? Nothing special happens to the file. > A common BASE1 user error is mixing up what is in ch1 and ch2. > In problem solving, I often want to see what file format I used to parse > that raw file into a raw Bioassay. I can't find that information in BASE2. > Where is it? It is not stored (*). > Also i want to see what sample I assigned to ch1 and ch2. I could not find > this information in BASE2. The link to samples was mainly used for getting access to annotations in the analysis part. In BASE 2 the annotation system is very different from the BASE 1 annotation system, and the link to samples has been replaced with (inherited) annotations at the raw bioassay level. > And when I make a new hybridization and adding > two samples, I am not forced to assign the labeled extracts to channels as > in BASE1. What is the definition of ch(1) and ch(2) in BASE2? I don't think there is any. > How do I now that my ratio is A/B and not B/A? The ratios are calculated with Formula items. BASE ships with a formula for calculating ch(1) / ch(2) but it is easy to change that or create another formula which instead does ch(2) / ch(1). /Nicklas (*) The information is stored as parameters to the job that imported the data but there is no way to easily query that information. In theory you can check all jobs which involved running an import plug-in and had a specific raw bioassay as one of it's parameters. Then, check the other parameters for info about file, file format, etc. Since jobs can be deleted, this would not be a very stable solution... ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
