Bob MacCallum wrote: > Hi again, > > Now that the festive season is well and truly over, I wonder if > anyone can help me out with my question (see below).
Festive season over? Does that mean I have to go back to work now? ;-) > > How would I set up a filter which would "give me all the genes/reporters > that > > are at least A times overexpressed in hyb. X AND at least B times > > underexpressed in hyb. Y"? I _wish_ I could say that that's easily done in BASE, but we never got around to making the filtering system as complex as it needs to be. There is a way to do it without resorting to plugins, but it involves heavy (ab)use of reporter lists: Looking at the data in hyb X (the 'expression value table' for that bioassay) you can filter the data and create a reporter list of the matches, and likewise for hyb Y. Then it is possible to filter the whole bioassayset against those reporter lists. Even worse: You could express more complicated logic functions (e.g. (A or B) and C) by creating reporter lists from filtering on reporter lists, but since filters are always ANDed, you'd have to express (A or B) as (NOT (NOT A AND NOT B)), by a whole series of filtering operations. At this point, I'd rather use a plugin. > > The filters don't seem to apply an AND across multiple data sets. Also, I > > don't see how you combine biological and technical replicates into one data > > set. > > > > Do people normally do this type of analysis with plugins or external > software? I know there are some plugins in existence for merging bioassays and for filtering data. Johan Enell has made some, and he's also managing the plugin archive, but there's not much there since the HD crash 5 months ago. If you bug him at johan.enell (at) med.lu.se, he might make something available. //Carl -- Carl Troein - [EMAIL PROTECTED] http://www.thep.lu.se/~carl/ ------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
