[base] 2D loess plug-in

Hi, Is there a 2D loess plug-in available for BASE? There used to be a page which listed some/all the plug-ins but now I can't find it. Regards, Steve --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that exte

Re: [base] BASE 2.0 RC2 released

Hi, > > I am happy to announce that BASE 2.0 RC 2 is now available for download: > http://lev.thep.lu.se/trac/base/wiki/DownloadPage > > Installation instructions are available at the BASE2 home page: > http://lev.thep.lu.se/trac/base/wiki It's good to see BASE2 is progressing! I notice Affy sup

[base] BASE 1.2.10 to 1.2.17

Hi, We have recently upgraded to BASE 1.2.17 (from BASE 1.2.10) in preparation for moving to BASE2. From the web interface, for all experiments under 'Experiments' under the 'Info' tab I get the error message: Error: No Property described for legacy column experimentType Please contact admini

Re: [base] BASE 1.2.10 to 1.2.17

> shouldn't be there if you've upgraded to the official 1.2.17 release... > Ok. Thanks. In terms of migrating to BASE2 though, will it make a difference? Kind Regards, Steve > Cheers, > Kjell > > Steve Taylor wrote: > >>Hi, >> >>We have recently

Re: [base] BASE 1.2.10 to 1.2.17

Hi Kjell and Nicklas, >>> It might look like you've updated to the latest CVS instead of the official latest release 1.2.17 ? The error message is related to the code related to MAGE-ML export to be released as part of 1.2.18. The error message should be harmless, but s

[base] Changing CDF/CEL association

Hi, Using BASE2 on (on the demo site) I accidentally associated the wrong CDF file with the CEL file. It looks like you should be able to change 'Array design' in 'Raw bioassay' but if you 'Edit' there doesn't appear to be an option to change it. Is there a work around or do I have to delete t

[base] Problem on converting plug-ins on BASE 1.2.10 to 1.2.17

Hi, I am moving over from BASE 1.2.10 (Solaris 9) to 1.2.17 (Fedora) and ultimately to BASE2. At the moment I can't seem to run some of the plug-ins in 1.2.17 though they work fine on 1.2.10. For example: On running MGH: avg channel intensity, I get the error: Plug-in output Failed to prepar

Re: [base] Problem on converting plug-ins on BASE 1.2.10 to 1.2.17

Hi, I have been investigating this further. The problem appears to be during the execution of baseFileReformatter. The header of my input file for this looks like: BASEfile section reformatter format normalBASEfile nanString numericFields intensity1 intensity2 fieldCount 2 a

[base] batchimporter

Hi, I just tried adding batchdataimporter to BASE 2.1.1 (build #2996; schema #20) using the instructions on http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/scri/batchimporter/README.txt but the plug-in does not show up in the Plugins list. I tried to add it again (just in case I ha

Re: [base] batchimporter

Hi Micha, > > Not sure what's gone wrong there -- I have added the plugin to > installations of both 2.1.1 and 2.2.1 and it worked fine. It also seems > to have worked okay for the other people who have tried it out so far, > so I am not sure what's happening. > > As far as I know the only thin

[base] 1.2 plugins

Hi, Can anyone confirm if it is possible to run BASE 1.2 plugins reliably in BASE 2+? I noticed on the web site it says: "Plug-ins created for BASE 1.2 can be made to work in BASE 2 using the Base1PluginExecuter plug-in (this is still in development phase)." Also is TMEV planned to be integrat

Re: [base] 1.2 plugins

way of capturing and keeping all the data in one place. I realise it may require some more hacking of TMEV but it would be a fantastic feature... > I forgot to add our customized version of MeV to BASE-hacks page. I'll > add the code to BASE-hacks. > > Ok thanks. Steve

[base] Batch Importer suggestion and broken image links

Hi, I have successfully got batch importer to run and it works very well. My question is are users always required to upload the CDF file - even if that CDF is stored already in BASE? Would it be possible to have a configuration option to specify the CDF in a drop down populated from the entri

Re: [base] Batch Importer suggestion and broken image links

Hi, >> >> I have successfully got batch importer to run and it works very well. >> My question is are users always required to upload the CDF file - >> even if that CDF is stored already in BASE? Would it be possible to >> have a configuration option to specify the CDF in a drop down >> populated f

Re: [base] BASE 2 & Illumina arrays

Hi, Can Jeremy (or anyone else) please give a link raw-data-types.xml they used for Illumina and perhaps the R script that was mentioned in this thread. I have written a perl script to do the splitting so it would be good to compare notes and reach a consensus. Is anyone on the list looking at w

Re: [base] Error running RMAExpress plug-in

Hi Cris, > > I am trying to run the RMAExpress plug-in to import Affymetrix data, but > I get the following error: > > net.sf.basedb.core.BaseException: Unable to import root bioassay. > at se.lu.thep.affymetrix.RMAExpress.storeResult (RMAExpress.java:424) > at se.lu.thep.affymetrix.RMAExpress.

Re: [base] BASE 2 & Illumina arrays

ml and extended-properties.xml do not appear to be different from the standard ones in BASE. Please can you check? Thanks! Steve > Jeremy > > > On 3/7/07, *Nicklas Nordborg* <[EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>> wrote: > > Steve Taylor wrote: >

Re: [base] BASE 2 & Illumina arrays

Plugin failed: java.lang.Exception: no suitable plugin configuration found for this data type The plugin works fine for Affy data and I can import Raw Bioassays individually. Also the experiment I am importing into is of type 'Illumina'. Thanks for any help, Steve > > Jeremy > >

Re: [base] BASE 2 & Illumina arrays

em was permissions. Even though I had defined a raw data type 'Illumina' I hadn't shared it with everyone. I can now batch import Illumina data. Thanks, Steve > > Jeremy > > On 3/9/07, *Steve Taylor* <[EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>>

Re: [base] Questions on Reporter IDs

Hi, > >>Thanks I found the link and now I can remove reporters. My problem now >>is that I have 3 reproters to delete and the system allows me to >>delete a max of 99 each time, the max number reporters displayed per >>page, but my selection is higher. Is there a way to delete all my >>se

Re: [base] Base1PluginExecuter

Johan Enell wrote: > I think it's best to discuss this in a new thread. > > The easiest way to go around this bug is to define a directory for the > Experiment. Edit Experiment and add a directory. Ok, thanks. That got me a bit further... > > You will also need to change the field '_allIntensi

Re: [base] Base1PluginExecuter

I just have to > make the import part a little bit more sensible. You can reopen a ticket > on the edit page but don't if you don't intend to follow up the > discussion. As I see it, the bug in ticket 511 is fixed. > Yes. 511 is fixed. Thanks, Steve > > /Johan > &g

[base] file format matching problems

Hi, I got a confusing message when I was using the Experiments > Import. Basically, BASE was expecting a zip file and I was (perhaps stupidly) trying to upload a single file. The BASE WWW interface returned: 'We couldn't find any file format mathing the file /home/Admin/latestbluefuse.txt.' I

Re: [base] file format matching problems

Hi Nicklas, >> >>I got a confusing message when I was using the Experiments > Import. >>Basically, BASE was expecting a zip file and I was (perhaps stupidly) >>trying to upload a single file. The BASE WWW interface returned: >> >>'We couldn't find any file format mathing the file >>/home/Admin/lat

Re: [base] file format matching problems

Nicklas Nordborg wrote: > Steve Taylor wrote: > >> Hi Nicklas, >> >>>> I got a confusing message when I was using the Experiments > Import. >>>> Basically, BASE was expecting a zip file and I was (perhaps stupidly) >>>> trying

[base] Data truncation: Out of range value

Hi, I have extended BASE2.2.1 (MySQL Distrib 5.0.27) to accept ScanArray files (very similar to GenePix) by changing extended-properties.xml and updating the database. The extended-properties.xml the intensity formula I am using is:

Re: [base] Data truncation: Out of range value

Hi Nicklas, > I think you have mailed or filed a bug reporter about a similar problem > before. See ticket #520: http://base.thep.lu.se/ticket/520 Ah, yes it's the same problem...thanks for fixing it. > > The problem was fixed in 2.2.3 so you need to upgrade your BASE > installation to somethin

Re: [base] BatchDataImporter broken w/ 2.4?

Hi, > I haven't installed BASE 2.4 as yet -- will give it a go this afternoon > and try out the batch importer with it. > > I have to admit to not having done any of the fixes/feature enhancements > to the batch importer that were requested, quite simply because I was > waiting for the Tab2MageI

[base] Importing Illumina format data in 2.4.1.

Hi, We have just updated to BASE 2.4.1 and I have tried importing an Illumina format file but I get the message: No file format that matches the file I tried Import via Experiment and used Import via Raw bioassays. In BASE 2.2.1 I set up BASE so it could import modified Illumina data using Je

Re: [base] Importing Illumina format data in 2.4.1.

Nicklas Nordborg wrote: > Steve Taylor wrote: > >>Hi, >> >>We have just updated to BASE 2.4.1 and I have tried importing an >>Illumina format file but I get the message: >> >>No file format that matches the file >> >>I tried Import via Exp

Re: [base] Importing Illumina format data in 2.4.1.

Nicklas Nordborg wrote: > Steve Taylor wrote: > > >>Thanks. The configuration looks good, unfortunately the plugin just >>hangs when I run it. It is just stuck on the 'Waiting' status. I have >>also tested a few other plugins and they do the same. There doesn

[base] New Plugins: Annotation importer problem

Hi, I have added the "Annotation Type and CV Loader" plugin and configured it as per the instructions. I can see Annotation importer on the Plugins screen. I have verified the the plugin accepts the test file at http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/AnnotationTypeCvImp