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]
Re: [base] BASE2 login error
Nicklas Nordborg wrote: The error seems to be related to the Recently view items menu. For some reason the string that holds the information has become corrupt and the code is unfortunately not able to handle this. The best advice I can give right now is to edit the basedir/www/include/menu.jsp to try to avoid the error. It is line 110 in this file that is causing the error. A temporary solution might be to change this to something like: int itemId = tmp.length 2 ? 0 : Values.getInt(tmp[1], 0); I'll try to check in a better fix in subversion tomorrow. There is now a fix available in the repository. Those who can't wait for 2.4.4 to be released can download the updated file: http://base.thep.lu.se/browser/branches/2.4-stable/www/include/menu.jsp?format=raw Replace the menu.jsp file inside basedir/www/include file with the downloaded file. /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]
Re: [base] BASE2 login error
Dear Nicklas, many thanks for the fast fix ! Cheerio, Reha Nicklas Nordborg wrote: Nicklas Nordborg wrote: The error seems to be related to the Recently view items menu. For some reason the string that holds the information has become corrupt and the code is unfortunately not able to handle this. The best advice I can give right now is to edit the basedir/www/include/menu.jsp to try to avoid the error. It is line 110 in this file that is causing the error. A temporary solution might be to change this to something like: int itemId = tmp.length 2 ? 0 : Values.getInt(tmp[1], 0); I'll try to check in a better fix in subversion tomorrow. There is now a fix available in the repository. Those who can't wait for 2.4.4 to be released can download the updated file: http://base.thep.lu.se/browser/branches/2.4-stable/www/include/menu.jsp?format=raw Replace the menu.jsp file inside basedir/www/include file with the downloaded file. /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] begin:vcard fn:Reha Yildirimman n:Yildirimman;Reha org:Max Planck Institute for molecular genetics;Lehrach AG Herwig adr:;;Ihnestr. 63-73;Berlin;;14195;Germany email;internet:[EMAIL PROTECTED] tel;work:+49-30-84131277 url:http://www.molgen.mpg.de version:2.1 end:vcard - 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]
