Re: [base] tab2mage exporter question
Hi Micha, Micha Bayer wrote: Hi Dominic, We are trying to export our first experiment for real so we can submit it to ArrayExpress, and initially it looked like everything had worked okay. But now we have found an error with the annotation that I wanted to ask you about. Our experiment is a two-colour one, and we have a factor which can take the value of mutant or wildtype. Both mutant and wildtype sample is applied to the hybridization (one per channel) and we then want the RawBioAssay item to inherit its annotations. The only way we could find to do that was to inherit from both the samples, but then only one of them is exported into the tab2mage file, which presumably is not good enough for ArrayExpress. This is becuase BASE chooses the first of the inherited annotations values that it finds for sample, assigns and displays this as the factor value for the experiment. And the tab2mage exporter exports this assigned value during export. I will post this response on the mailing list so that Nicklas and others can pick it up. I reckon we should list the inherited values for two channel raw bioassay on the experiment page (at the raw bio assay section. And then we can find a mechanism to export that. I think array express will accept the exported file as it is. Although there will be a loss of information. I.e. instead of having mutant and wildtype as factor value on each Hyb channel row of the tab2mage file, you will only have either one that Base has assigned as factor value. ¬Dominic - 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] tab2mage exporter question
Dominic Oyeniran wrote: Hi Micha, Micha Bayer wrote: Hi Dominic, We are trying to export our first experiment for real so we can submit it to ArrayExpress, and initially it looked like everything had worked okay. But now we have found an error with the annotation that I wanted to ask you about. Our experiment is a two-colour one, and we have a factor which can take the value of mutant or wildtype. Both mutant and wildtype sample is applied to the hybridization (one per channel) and we then want the RawBioAssay item to inherit its annotations. The only way we could find to do that was to inherit from both the samples, but then only one of them is exported into the tab2mage file, which presumably is not good enough for ArrayExpress. This is becuase BASE chooses the first of the inherited annotations values that it finds for sample, assigns and displays this as the factor value for the experiment. BASE doesn't choose one of them. All inherited annotation values are always displayed. /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] tab2mage exporter question
Nicklas Nordborg wrote: Dominic Oyeniran wrote: Hi Micha, Micha Bayer wrote: Hi Dominic, We are trying to export our first experiment for real so we can submit it to ArrayExpress, and initially it looked like everything had worked okay. But now we have found an error with the annotation that I wanted to ask you about. Our experiment is a two-colour one, and we have a factor which can take the value of mutant or wildtype. Both mutant and wildtype sample is applied to the hybridization (one per channel) and we then want the RawBioAssay item to inherit its annotations. The only way we could find to do that was to inherit from both the samples, but then only one of them is exported into the tab2mage file, which presumably is not good enough for ArrayExpress. This is becuase BASE chooses the first of the inherited annotations values that it finds for sample, assigns and displays this as the factor value for the experiment. BASE doesn't choose one of them. All inherited annotation values are always displayed. BASE actually chooses one of them, at least as shown on the GUI here. It's not the exprimental factors section of the GUI parse that's relevant here, based on my understanding, but the Raw Bio assays section listing each raw bio assay included in the experiment. Since experimental factor values/annotation values has to be propagated through the Raw Bio assays. For each Raw Bio assay in an experiment, you can only see or get one of the inherited values having inherited annotations from two different Sample items each from a line in the two channel hyb. However, the inherited values are displayed as separate annotations for the raw bio assays on the 'Inherited annotations and protocol parameters section' of the view page. If this is not the case then I must have a wrong understanding of how factor values annotation are obtained or handled in BASE. ¬Dominic - 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] Problems running Tab2Mage Importer, NOT sufficient Disk Space
I had this problem too, but had not yet got round to figuring out the solution. It is very helpful to read the README.TXT file on the BasePlugins download page before using the tab2mage importer plugin to avoid any issues /problems. The direct link to the file as stated in the last email is : http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/README.txt. Just an information for other interested users too. Thanks, ¬Dominic Bob MacCallum wrote: Dominic Oyeniran writes: vegard nygaard wrote: I am trying out the Tab2Mage importer. When starting it from the import button in an experiment it quickly returns with an error. I am running it as root on base2.4.3 having added tab2mage importer and Annotation Type and CV Loader as plug-ins. Input file is the genepix example file found at http://www.ebi.ac.uk/~oyeniran/pages/download.html. This is output from the plugin window: Name Run plugin: Tab2Mage Importer Description Priority 4 (1 = highest, 10 = lowest) Status Error: IMPORT FAILS: The directory containing the unzipped files could not be found. You may NOT have sufficient Disk Space Percent complete 100% This is a known issue and has been documented here: http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/README.txt. Please scroll to the usage section right after the installation section. Simply, we recommend not running the importer as the root user. I believe it's advisable to run BASE as an administrator and not the root user as well. In the next release of the importer, a root user will be able to run the importer as well. In my efforts to solve the problem I wanted to inspect the code but was unable to find the java files referred in the stack trace. Where can I find them? In the jar file I found only class files. I downloaded the whole Nutribase-2.0.2-src.zip, but was unable to unpack the file properly. Are the source files for the importer inside and if so how do I unpack the zip file? The source file for the importer is available at: http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/src/uk/ - 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] - 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] Problems running Tab2Mage Importer, NOT sufficient Disk Space
And it is also linked from http://lev.thep.lu.se/trac/baseplugins/wiki/uk.ac.ebi.Tab2MageImporter But the readme file is not very precise about this problem, it advices me not to use root. I disregarded that advice :(. If it will only run as a non-root user with a limited quota, that should be stated as an imperative. Changed and checked in. Anyways, I got past that problem now but ran into another one. Error: IMPORT FAILS: The tab2mage file supplied is not compliant with the tab2mage specification I use the genepix example zip file. If this is another known issue please let me know, if not I will look more into it in detail tomorrow and let you know if I am stuck. Please check the exceptions on the server and send it to me to have a look at. ¬Dominic - 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] BASE 2.4.4 released. Please read, important performance issue fixed in this release.
That is excellent news. I was thinking that the root bioassay set creation was rather too slow for a simple subtraction that takes no time in BASE1. many thanks, Bob. Jari Häkkinen writes: We are happy to announce the release of BASE 2.4.4. As always you can find the latest release at http://base.thep.lu.se/wiki/DownloadPage for download. This releases contains an important fix that resolves severe performance issues, cf. http://base.thep.lu.se/ticket/796. The code is now fixed but you will have to update your database, please read http://base.thep.lu.se/chrome/site/latest/html/admindoc/installation_upgrade/installation_upgrade.upgrade.html on how to update your database. We have not detected any data integrity problems related to this issue. The script may take quite some time depending on your database size. Our BASE installation took almost 24h to fix, so patience is a virtue here. Remember to upgrade BASE before starting the upgrade script and kepp BASE shutdown until the script ends. Happy BASEing, The Lund BASE team - 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] -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED] - 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] Problems running Tab2Mage Importer, NOT sufficient Disk Space
Just for your information: Dominic Oyeniran wrote: This is a known issue and has been documented here: http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/README.txt. Please scroll to the usage section right after the installation section. We prefer to use links to the more generic http://baseplugins.thep.lu.se since lev is merely the current host of the baseplugins (and base) and it may changes in the future. That is the above link should be a more archive safe http://baseplugins.thep.lu.se/browser/trunk/uk/ac/ebi/Tab2MageImporter/README.txt - 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]
