Re: [base] Base 1.2 plugin - Virtual Array -1.1
Thanks that worked and am now able to see and run the Virtual Array plugin. Unfortunately the plugin also fails with an error when running: Error: Error during export: Item not found: Unknown reporter field: reporter (you can add this field as an formula) Thanks again for all your help, Thomas On 03/14/2011 07:27 AM, Nicklas Nordborg wrote: On 2011-03-11 18:13, Thomas Person wrote: Ok, I guess I'm missing something in the configuration of the plugin, for all the plugins associated with the Base1PluginExecuter. If i simply create the plugin under the Base1PluginExecuter but then not configure it, then I am given the option under the drop down to run it when attempting Run an analysis plugin but it does not function as it hasn't been configured. Oh... I guess we have to look into that. Unconfigured plug-in shouldn't really be in that list. But once i do configure it, with the proper file and path to the run command. the option to run the plugin in the drop down under run an analysis plugin disappears as an option to run. We have checked the installation procedure of the VirtualArray plug-in and it turns out that the configuration file that is used is incorrect. The problem with the 'descr' field has already been fixed but there are two more issues: * The 'geneAverages' setting should be '1', not '0'. * The 'minChannels' setting should be '1', not '2'. Fortunately both settings can be changed in the web gui. Start the configuration wizard for the VirtualArray plug-in. In the first step, make sure to NOT select a file. This will take you to a second step where you can change the value for the two parameters mentioned above. The 'geneAverages' setting is called 'Average on reporters' in the wizard. Hope this works better. /Nicklas -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Base 1.2 plugin - Virtual Array -1.1
On 2011-03-11 18:13, Thomas Person wrote: Ok, I guess I'm missing something in the configuration of the plugin, for all the plugins associated with the Base1PluginExecuter. If i simply create the plugin under the Base1PluginExecuter but then not configure it, then I am given the option under the drop down to run it when attempting Run an analysis plugin but it does not function as it hasn't been configured. Oh... I guess we have to look into that. Unconfigured plug-in shouldn't really be in that list. But once i do configure it, with the proper file and path to the run command. the option to run the plugin in the drop down under run an analysis plugin disappears as an option to run. We have checked the installation procedure of the VirtualArray plug-in and it turns out that the configuration file that is used is incorrect. The problem with the 'descr' field has already been fixed but there are two more issues: * The 'geneAverages' setting should be '1', not '0'. * The 'minChannels' setting should be '1', not '2'. Fortunately both settings can be changed in the web gui. Start the configuration wizard for the VirtualArray plug-in. In the first step, make sure to NOT select a file. This will take you to a second step where you can change the value for the two parameters mentioned above. The 'geneAverages' setting is called 'Average on reporters' in the wizard. Hope this works better. /Nicklas -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Base 1.2 plugin - Virtual Array -1.1
Ok, I guess I'm missing something in the configuration of the plugin, for all the plugins associated with the Base1PluginExecuter. If i simply create the plugin under the Base1PluginExecuter but then not configure it, then I am given the option under the drop down to run it when attempting Run an analysis plugin but it does not function as it hasn't been configured. But once i do configure it, with the proper file and path to the run command. the option to run the plugin in the drop down under run an analysis plugin disappears as an option to run. Thanks again Thomas From: Nicklas Nordborg [nick...@thep.lu.se] Sent: Thursday, March 10, 2011 4:01 PM To: basedb-users@lists.sourceforge.net Subject: Re: [base] Base 1.2 plugin - Virtual Array -1.1 On 2011-03-10 20:58, Jari Häkkinen wrote: Also, Virtual array works only on 2-channel data. I was never involved in the development of this plug-in so maybe I am missing something obvious I had a quick lock at the code (http://baseplugins.thep.lu.se/browser/plugins/base1/se.lu.onk.VirtualArray/trunk/src/virtualarray/VirtualArray.java) and I can't see anything in it that depends on the number of channels. As far as I can tell it is simply copying the input intensities to the output without change. The only difference is that it assigns negative position numbers. Actually I don't see any point in running the VirtualArray at all. All intensity data afterwards will be exactly the same as it was before. The only change is that position numbers are different, and as a side-effect of that the connection to raw data is lost. But... maybe I am missing something obvious... Anyone knows more about this? In any case, since there is not any dependency on the number of channels in the code, it should be safe to change 'minChannels 2' to 'minChannels 1' in the pluginVirtualArray.base file. Or (easier) directly by reconfiguring the plug-in in the web interface. There should be an option for this setting in the second step (leave the file field empty in the first step). /Nicklas -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net UT Southwestern Medical Center The future of medicine, today. -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Base 1.2 plugin - Virtual Array -1.1
Are you sure that all prerequisites are met? The plug-in configuration and the Base1PluginExecutor should be shared appropriately. Also, Virtual array works only on 2-channel data. Jari On 2011-03-10 17.25, Thomas Person wrote: Thanks! That change allows installation but once I atmpt to use the plugin, by clicking on the Run an Analysis Plugin icon when looking at an experiment under Bioassay set, the option select the the plugin in the drop down menu does not appear. Thanks again, Thomas From: Nicklas Nordborg [nick...@thep.lu.se] Sent: Wednesday, March 09, 2011 1:11 AM To: BASE ML Subject: Re: [base] Base 1.2 plugin - Virtual Array -1.1 On 2011-03-08 22:28, Thomas Person wrote: Howdy All, I'm attempting to install the Virtual Array 1.1 plugin on my Base 2.15 server. I get two sets of errors. ( I was able to install the Center-2.1 Plugin with no error). Thanks for the report. I can verify that the VirtualArray plug-in can't be installed as is. There seems to be a bug in BASE that is related to the 'descr' field in the 'pluginVirtualArray.base' file. This file has a space instead of a tab character between the 'descr' and the rest of the line. Please change the space to a tab and then re-try the installation. /Nicklas -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net UT Southwestern Medical Center The future of medicine, today. -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Base 1.2 plugin - Virtual Array -1.1
The only prerequisite I saw was BaseFile, and thats already included with Virtual Array, correct? Yeah, I think its all shared out appropriately, course I'm also still only using the root user for the server. Still testing everything before I deploy it for all my users and create them accounts. Since we don't have two channel data, we have Illumina bead Chip, I guess this issue is a moot point for me. But leaves me with the question, is there another way to average the signal of arrays at the server? My users will often have 4 experimental arrays and 4 control arrays for each of their 5 or more different time points. And want to be able to easily view graphs and compare the control to the experimental. True we can do some basic processing between base and MeV or whatever they want to use, but its not that easy. Thanks again for all the help, Thomas From: Jari Häkkinen [j...@thep.lu.se] Sent: Thursday, March 10, 2011 1:58 PM To: basedb-users@lists.sourceforge.net Subject: Re: [base] Base 1.2 plugin - Virtual Array -1.1 Are you sure that all prerequisites are met? The plug-in configuration and the Base1PluginExecutor should be shared appropriately. Also, Virtual array works only on 2-channel data. Jari On 2011-03-10 17.25, Thomas Person wrote: Thanks! That change allows installation but once I atmpt to use the plugin, by clicking on the Run an Analysis Plugin icon when looking at an experiment under Bioassay set, the option select the the plugin in the drop down menu does not appear. Thanks again, Thomas From: Nicklas Nordborg [nick...@thep.lu.se] Sent: Wednesday, March 09, 2011 1:11 AM To: BASE ML Subject: Re: [base] Base 1.2 plugin - Virtual Array -1.1 On 2011-03-08 22:28, Thomas Person wrote: Howdy All, I'm attempting to install the Virtual Array 1.1 plugin on my Base 2.15 server. I get two sets of errors. ( I was able to install the Center-2.1 Plugin with no error). Thanks for the report. I can verify that the VirtualArray plug-in can't be installed as is. There seems to be a bug in BASE that is related to the 'descr' field in the 'pluginVirtualArray.base' file. This file has a space instead of a tab character between the 'descr' and the rest of the line. Please change the space to a tab and then re-try the installation. /Nicklas -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net UT Southwestern Medical Center The future of medicine, today. -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Base 1.2 plugin - Virtual Array -1.1
On 2011-03-10 20:58, Jari Häkkinen wrote: Also, Virtual array works only on 2-channel data. I was never involved in the development of this plug-in so maybe I am missing something obvious I had a quick lock at the code (http://baseplugins.thep.lu.se/browser/plugins/base1/se.lu.onk.VirtualArray/trunk/src/virtualarray/VirtualArray.java) and I can't see anything in it that depends on the number of channels. As far as I can tell it is simply copying the input intensities to the output without change. The only difference is that it assigns negative position numbers. Actually I don't see any point in running the VirtualArray at all. All intensity data afterwards will be exactly the same as it was before. The only change is that position numbers are different, and as a side-effect of that the connection to raw data is lost. But... maybe I am missing something obvious... Anyone knows more about this? In any case, since there is not any dependency on the number of channels in the code, it should be safe to change 'minChannels 2' to 'minChannels 1' in the pluginVirtualArray.base file. Or (easier) directly by reconfiguring the plug-in in the web interface. There should be an option for this setting in the second step (leave the file field empty in the first step). /Nicklas -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Base 1.2 plugin - Virtual Array -1.1
On 2011-03-08 22:28, Thomas Person wrote: Howdy All, I'm attempting to install the Virtual Array 1.1 plugin on my Base 2.15 server. I get two sets of errors. ( I was able to install the Center-2.1 Plugin with no error). Thanks for the report. I can verify that the VirtualArray plug-in can't be installed as is. There seems to be a bug in BASE that is related to the 'descr' field in the 'pluginVirtualArray.base' file. This file has a space instead of a tab character between the 'descr' and the rest of the line. Please change the space to a tab and then re-try the installation. /Nicklas -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
