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]
