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]
