Missed to answer you other questions... You use the gene filter "In # of Assays"
Exampel: You have 4 assays and you want to filter out the spots with ratio greater then 2 in at least 3 assays. You need two criterias for this. The spot filter "ratio > 2" and the and the gene filter "In # Assays > 2" /Johan Bob MacCallum wrote: > Hi all, > > In the analysis steps part of BASE 1.2.x, is there a way to create a reporter > list such that X out of Y assays satisfy some filter condition, > where 1 < X < Y ? > > I already know how to do it where X=1 or X=Y. For example: > > 1. Reporters where at least one assay has a twofold change > Filter on "ratio not between 0.5, 2", create reporter list R with results, > then filter original set on "reporter list present in R". > > 2. Reporters where *all* assays have max intensity >= 100: > Filter on "max(Ch1,Ch2) < 100", create reporter list S with results, > then filter original set on "reporter list absent in S". > > Quite often you want to filter somewhere in between, i.e. at least half of the > assays should show X-fold changes, or whatever. > > It would not be hard to write a plugin to do this, but I haven't written any > plugins yet. So I wondered if there were any GUI tricks I had missed. > Failing that I'll write a pseudo-plugin (a script which takes a custom BASE > file and dumps a reporter list) and worry about configuring it as a plugin at > a later date. > > Also, if anyone has an 'averaging over replicates' plugin (based on a > specified sample annotation), I would be very grateful. Installing such a > plugin would help me figure out how to write one. > > cheers, > Bob. > > ------------------------------------------------------------------------- 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.php&p=sourceforge&CID=DEVDEV _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
