YANNICK wrote: > Hi BASE2 users! > > I am using BASE 2.11 and have some questions. > I want to calculate Ratios from 2 bioassays organized as following: > - 1st bioassay = control > - 2nd = treatment > Labellings are performed as following: > Cy5= pool of all samples extracts. Same in all arrays (serves for > normalizations between arrays) > Cy3= experimental condition. > > Here are my questions: > - is it possible to perform Rquantile normalization (cf > normalizeBetweenArrays, R Bioconductors)?
You should have a look at http://baseplugins.thep.lu.se/wiki/net.sf.basedb.normalizers and the associated milestone tickets for the next release of the package, http://baseplugins.thep.lu.se/query?milestone=net.sf.basedb.normalizers+1.1&order=priority It provides a few more normalization methods of which quantile normalization is already available, and qQuantile normalization is planned for the next release of the package. You need to compare these normalizers to the ones provided by Bioconductor normalizeBetweenArrays. Obviously R-G quantile is not supported since the methods in net.sf.basedb.normalizers only work on ratios. The normalizer package discussed here does not target your issue with mixing ratios between assays ... contributions are welcome. Cheers, Jari > - And how to calculate ratios for each reporter? we must calculate > ratios of cy3 intensities between the two bioassays. (e.g. > ch(2)[biaoassay1] / ch(2)[bioassay2]). > > Could someone help me? > thanks! > > yannick lippi > -- > ---------------------------------------------------------- > Equipe Interactions Plantes-Microorganismes > UMR 5546 CNRS/Université P. Sabatier > Pôle de Biotechnologies Végétales > 24, chemin de Borde Rouge B.P. 17 Auzeville > 31 326 CASTANET-TOLOSAN FRANCE > ---------------------------------------------------------- > > ------------------------------------------------------------------------------ > Stay on top of everything new and different, both inside and > around Java (TM) technology - register by April 22, and save > $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco. > 300 plus technical and hands-on sessions. Register today. > Use priority code J9JMT32. http://p.sf.net/sfu/p > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > basedb-users-requ...@lists.sourceforge.net ------------------------------------------------------------------------------ Stay on top of everything new and different, both inside and around Java (TM) technology - register by April 22, and save $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco. 300 plus technical and hands-on sessions. Register today. Use priority code J9JMT32. http://p.sf.net/sfu/p _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
