Re: [base] BASE 2 Illumina arrays
Nicklas Nordborg wrote: Jeremy Davis-Turak wrote: I have implemented the incorporation of Illumina data into our BASE system, along with a raw data importer. Our version requires that the gene_profile.csv be split up into separate files, which we have done with an R script. This can also be done manually in excel, or feasibly in a BASE script. Nicklas, how do I share the plugin configurations with others? I have created a ticket in our trac system for this issue: http://base.thep.lu.se/ticket/486 Everyone are welcome to comment and it is also possible to attach files to it. Note that you have to be logged in before you can comment or upload files. Use base/base as username/password. I think the best solution would be to have a BASE plugin that can split the file automatically and the import the raw data in one go. If that is possible or not I don't know since I have no knowledge of the file format. We have planned to include the Illumina import plug-in in the next release (2.4). We have not been able to find any good description of the file format or example data files. Does anybody out there have any information to help us implement this? We definitely need one or more example data files that we can use for testing. The files will be put in a protected repository that is only available to the core developers. It would also be nice to have a more formal description, or at least a short overview, of the file format. Since it is only 3 weeks to go before 2.4 is released we need any information as soon as possible (this week!). /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]
[base] svn check out of BASE2 WS enabled
Hi all, I try to download to webservices enabled version of BASE with svn as mentioned on the plugins page (http://baseplugins.thep.lu.se/wiki/se.lu.thep.webservices_clients). When I check out the web services branch (svn co http://lev.thep.lu.se/repository/base/branches/webservices BASE-webservices) , I always get the same error : svn: REPORT request failed on '/repository/base/!svn/vcc/default' svn: REPORT of '/repository/base/!svn/vcc/default': 400 Bad Request (http://lev.thep.lu.se) Does anyboby have already tried to get this version ? Thanks Virginie - 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] svn check out of BASE2 WS enabled
Virginie Garcia wrote: Hi all, I try to download to webservices enabled version of BASE with svn as mentioned on the plugins page (http://baseplugins.thep.lu.se/wiki/se.lu.thep.webservices_clients). When I check out the web services branch (svn co http://lev.thep.lu.se/repository/base/branches/webservices BASE-webservices) , I always get the same error : svn: REPORT request failed on '/repository/base/!svn/vcc/default' svn: REPORT of '/repository/base/!svn/vcc/default': 400 Bad Request (http://lev.thep.lu.se) Does anyboby have already tried to get this version ? I just tried it and it works for me. I searched the net for similar problems and most of them seemed to be related to the user beeing behind a proxy that doesn't pass on all types of requests. Check for example this link: http://lists.ipython.scipy.org/pipermail/ipython-dev/2005-September/001737.html A suggested workaround is to change the http:// to https:// /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] svn check out of BASE2 WS enabled
OK. It works fine with https. Thanks a lot. Virginie Nicklas Nordborg a écrit : Virginie Garcia wrote: Hi all, I try to download to webservices enabled version of BASE with svn as mentioned on the plugins page (http://baseplugins.thep.lu.se/wiki/se.lu.thep.webservices_clients). When I check out the web services branch (svn co http://lev.thep.lu.se/repository/base/branches/webservices BASE-webservices) , I always get the same error : svn: REPORT request failed on '/repository/base/!svn/vcc/default' svn: REPORT of '/repository/base/!svn/vcc/default': 400 Bad Request (http://lev.thep.lu.se) Does anyboby have already tried to get this version ? I just tried it and it works for me. I searched the net for similar problems and most of them seemed to be related to the user beeing behind a proxy that doesn't pass on all types of requests. Check for example this link: http://lists.ipython.scipy.org/pipermail/ipython-dev/2005-September/001737.html A suggested workaround is to change the http:// to https:// /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] BASE 2 Illumina arrays
Hi Nicklas, I uploaded some data files to the Ticket. Here is a brief summary of what the data looks like: 1) Annotation data: CSV file. It's too bad that it's a CSV, because some of the fields contain commas! 2) Data: (header is on ~ line 8) a) For each set of chips that are processed at the same time, there is one resulting file. Thus, if you did two rat chips (each of which has 12 arrays on them), you would have 24 arrays contained in one file. b) Depending on the settings of the software at the time of scanning, you can have somewhere from 1-8 data columns per array (I don't know the exact range, but I know that it's variable). c) The first column contains the probe IDs, the rest of them are data. d) Each data column name is a concatenation of 3 things: i) The data type (i.e. 'AVG_Signal' or 'BEAD_STDEV') ii) The chip number (10 digits) iii) A capital letter indicating the position of the array on the chip (i.e. A-F for human, A-H for mouse, or A-L for rat.) EXAMPLE: the first 8 columns in my rat file are: AVG_Signal-1677718123_A BEAD_STDEV-1677718123_A Avg_NBEADS-1677718123_A Detection-1677718123_A AVG_Signal-1677718123_B BEAD_STDEV-1677718123_B Avg_NBEADS-1677718123_B Detection-1677718123_B and a number of columns later, they transition smoothly to the next chip: Avg_NBEADS-1677718123_L Detection-1677718123_L AVG_Signal-1677718142_A BEAD_STDEV-1677718142_A In my R script, you have to hard-code the number of data columns per array, and the number of arrays per chip. Thanks for making this plugin! Jeremy On 7/31/07, Nicklas Nordborg [EMAIL PROTECTED] wrote: Nicklas Nordborg wrote: Jeremy Davis-Turak wrote: I have implemented the incorporation of Illumina data into our BASE system, along with a raw data importer. Our version requires that the gene_profile.csv be split up into separate files, which we have done with an R script. This can also be done manually in excel, or feasibly in a BASE script. Nicklas, how do I share the plugin configurations with others? I have created a ticket in our trac system for this issue: http://base.thep.lu.se/ticket/486 Everyone are welcome to comment and it is also possible to attach files to it. Note that you have to be logged in before you can comment or upload files. Use base/base as username/password. I think the best solution would be to have a BASE plugin that can split the file automatically and the import the raw data in one go. If that is possible or not I don't know since I have no knowledge of the file format. We have planned to include the Illumina import plug-in in the next release (2.4). We have not been able to find any good description of the file format or example data files. Does anybody out there have any information to help us implement this? We definitely need one or more example data files that we can use for testing. The files will be put in a protected repository that is only available to the core developers. It would also be nice to have a more formal description, or at least a short overview, of the file format. Since it is only 3 weeks to go before 2.4 is released we need any information as soon as possible (this week!). /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] - 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]
