Jan Feng wrote: > Dear BioArray development team, > [...] > We would like ask your opinion on LOWESS normalization and > whether your LOWESS normalization in the BioArray package > also assumes a zero-mean log ratio. Is it possible to apply > your package to our unique situation? > > We look forward to your prompt reply.
Hello Jan. The name of the project is BASE, with BioArray Software Environment more or less being a backronym - we were looking for a name that sounded reasonably cool and still meant something relevant. The easiest way to do what you want is probably to find the mean (or median or whatever) ratio, apply lowess, and then shift the ratios. It doesn't sound like you're actually using BASE, so you'd have to muck about with the normalizer code (in plugins/src/normalizers) to make it work in your pipeline. Which should be doable. Or use our funky BASEfile format, but if you're not using BASE that just seems wrong. Or you could start using BASE, but doing so just for a normalizer is a bit like contracting a Vogon contructor fleet to have them dig a small hole in your back yard - it works, but you'll get more than you bargained for. //Carl -- Carl Troein - [EMAIL PROTECTED] http://www.thep.lu.se/~carl/ BASE developer - http://base.thep.lu.se/ ------------------------------------------------------- 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]
