Re: [base] How can I associate Illumina data with hybs (and samples)
You can select which scan a raw bioassay belongs to from the Edit rawbioassay page. Thanks Nicklas, this was what I was looking for (but at the wrong place). In order for the importer to be really useful I need to connect the raw data to samples in some way. From reading earlier posts it seems that connecting all the raw bioassays to one single scan is possible, but will there in upcoming base versions be more flexible association possibilities? We have discussed this and came to the conclusion that the current implementation is the most accurate representation of the process. The BASE model assumes that there is a one-to-one relation between a slide and hybridization. An Illumina slide has several (8 or more) arrays on a single slide. This doesn't fit the current model in all aspects. Some compromises has to be made. This is how we decided to do: * The slide is represented a single ArraySlide item in the database * The hybridization event links 8 (or more) labeled extracts to the slide (one for each array) * A single scan event represents the scanning * One raw bioassay for each array is created This will make is possible to accurately record scan and hybridization parameters without having to duplicate (8 times) the same data. The drawback is that the experiment validation will complain about the 8 labeled extracts since it expects only 1 for 1-channel data. It will also complain about all labeled extracts having the same label. But these warnings can be turned off. Another drawback is that all 8 labeled extracts will be treated as parents to all 8 raw bioassays, even though there really is a one-to-one relationship between those. /Nicklas I don't mind those drawbacks as long as the user can connect to one hyb (and one sample indeirectly) from the Edit raw bioassay page. Vegard. - 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/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] How can I associate Illumina data with hybs (and samples)
Hi I am testing out the Illumina importer and have some questions. Can I connect the created raw bioassays to hybridizations (and indirectly to samples)? On the scan page I looked for a associate raw bioassay , but only found the new raw bioassay. In order for the importer to be really useful I need to connect the raw data to samples in some way. From reading earlier posts it seems that connecting all the raw bioassays to one single scan is possible, but will there in upcoming base versions be more flexible association possibilities? If the Illumina Importer cannot attach raw bioassays to samples I wonder if I can use the Tab2Mage Importer or BatchDataImporter with Illumina data? Best regards. Vegard Nygaard Software Engineer Department of Tumor Biology (Montebello) Rikshospitalet-Radiumhospitalet Medical Center 0310 Oslo Bioinformatics user support (NMC) Phone 0047 22935590 - 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/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] How can I associate Illumina data with hybs (and samples)
vegard nygaard wrote: Hi I am testing out the Illumina importer and have some questions. Can I connect the created raw bioassays to hybridizations (and indirectly to samples)? Yes. When you run the importer you have the option to select a scan that will be associated with the raw bioassays. The scan can be associated with a hybridization which is then associated with labeled extracts, and so on, up to samples. On the scan page I looked for a associate raw bioassay , but only found the new raw bioassay. You can select which scan a raw bioassay belongs to from the Edit rawbioassay page. In order for the importer to be really useful I need to connect the raw data to samples in some way. From reading earlier posts it seems that connecting all the raw bioassays to one single scan is possible, but will there in upcoming base versions be more flexible association possibilities? We have discussed this and came to the conclusion that the current implementation is the most accurate representation of the process. The BASE model assumes that there is a one-to-one relation between a slide and hybridization. An Illumina slide has several (8 or more) arrays on a single slide. This doesn't fit the current model in all aspects. Some compromises has to be made. This is how we decided to do: * The slide is represented a single ArraySlide item in the database * The hybridization event links 8 (or more) labeled extracts to the slide (one for each array) * A single scan event represents the scanning * One raw bioassay for each array is created This will make is possible to accurately record scan and hybridization parameters without having to duplicate (8 times) the same data. The drawback is that the experiment validation will complain about the 8 labeled extracts since it expects only 1 for 1-channel data. It will also complain about all labeled extracts having the same label. But these warnings can be turned off. Another drawback is that all 8 labeled extracts will be treated as parents to all 8 raw bioassays, even though there really is a one-to-one relationship between those. /Nicklas - 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/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
