Re: [base] Réplicates in base 2
Emmanuel Courcelle wrote: Hello We are trying to create an experiment composed with: -4 slides -3 times each reporter on each slide So, we have up to 12 replicates for each reporter (sometimes less because some flagged spots were filtered out). How to make a final bioassay set with 6158 averaged-spots instead of more than 77000 ? There is no merge plugin available for BASE2. You can try using the BASE1 merge plugin which can be found on: http://lev.thep.lu.se/trac/baseplugins/wiki/PluginDownload /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Location of original source files
Charles Girardot wrote: Hi Nicklas, I might have missed something as I am not using BASE2 now and haven't investigated in details. I have a comment on this thread : Very often people come up with some logics in naming their files and, in the context of re-exporting them (eg, submission), they like to see file having original names. They might be various other situation where having the same name is good. I think you should keep original names somewhere like in BASE1, it makes things easier. When you upload files the original filename is kept in the database. There is however no information that links a rawbioassay to the file that was used for importing the data. It has nothing to do with the file names. /Nicklas Am I off track? Cheers Charles On Dec 8, 2006, at 9:00 AM, Nicklas Nordborg wrote: Keith Ching wrote: Hi, I am trying to write a plugin that will download the original source files used to populate the RawBioAssay objects. When you import data into a RawBioAssay, is the name of the original source file saved somewhere in the database? I am at the point where i can select the RawBioAssays that i want to download. It's just I can't find what file was originally used to create it. That information is not saved. /Nicklas -- --- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php? page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] = Charles Girardot European Molecular Biology Laboratory C. Boulin and E. Furlong Groups Tel: +49-6221-387-8426 Email: [EMAIL PROTECTED] Meyerhofstrasse 1 - Postfach 10.2209 69012 Heidelberg, Germany = - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] Conversion from string to int after plate import
Hi, I'm importing the following plate information through the plate 384_wells import plate. 384_number 384_column 384_row 384_position oligo_id plate_1 1 A A1 SEQ12345 plate_1 2 A A2 SEQ12346 plate_1 3 A A3 SEQ12347 The importing works fine but the row letters are converted into strings and +1 is added to the column values. For example the row value A is converted into 0 and the col value 1 is converted into 0. Is this the expected behaviour ? How can i resolve this issus.? Also note the the testfile option available through the importer does get the values properly without changing anything. thanks , david - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Conversion from string to int after plate import
Hi, After checking the sql structure of the database I realized that the table PlateMappingDetails contains indeed int values for all fields. I would have imagined that one could eventually use a letter instead of an integer. What do you think ? - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Location of original source files
There is one place that i found the linkage of the RawBioAssay to the original file.. the job parameters.. when you import data into the RawBioAssay it creates a job that details the RawBioAssay and the file path.. however, users can delete the jobs and thus wipe out the connection.. ( which i have done as well ) however, we will soon be storing large files which will not be loaded into the database per se, but would like to retrieve them based on the meta data in BASE2.. thus no jobs will be created, unless i create a bogus plugin importer just to make a file to RawBioAssay connection. it seems less of a hack, but not much, to instead create an annotation field named File that describes the RawBioAssay and place the file path there. -keith Nicklas Nordborg wrote: Charles Girardot wrote: Hi Nicklas, I might have missed something as I am not using BASE2 now and haven't investigated in details. I have a comment on this thread : Very often people come up with some logics in naming their files and, in the context of re-exporting them (eg, submission), they like to see file having original names. They might be various other situation where having the same name is good. I think you should keep original names somewhere like in BASE1, it makes things easier. When you upload files the original filename is kept in the database. There is however no information that links a rawbioassay to the file that was used for importing the data. It has nothing to do with the file names. /Nicklas Am I off track? Cheers Charles On Dec 8, 2006, at 9:00 AM, Nicklas Nordborg wrote: Keith Ching wrote: Hi, I am trying to write a plugin that will download the original source files used to populate the RawBioAssay objects. When you import data into a RawBioAssay, is the name of the original source file saved somewhere in the database? I am at the point where i can select the RawBioAssays that i want to download. It's just I can't find what file was originally used to create it. That information is not saved. /Nicklas -- --- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php? page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] = Charles Girardot European Molecular Biology Laboratory C. Boulin and E. Furlong Groups Tel: +49-6221-387-8426 Email: [EMAIL PROTECTED] Meyerhofstrasse 1 - Postfach 10.2209 69012 Heidelberg, Germany = - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Keith Ching, Ph.D. Bioinformatics, Laboratory of Gene Regulation Ludwig Institute for Cancer Research 9500 Gilman Drive, #0653 CMM East, Room 3020 La Jolla, CA 92093-0653 [EMAIL PROTECTED] 858-822-5767 - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
