Hi Jari and Nicklas, Thanks for your answers about BASE! I have others questions...
__FIRST QUESTION: Pb for installing "Normalization plug-ins" package I followed instructions from the "install" file (http://baseplugins.thep.lu.se/browser/plugins/base2/net.sf.basedb.normalizers/trunk/INSTALL) - I have put the .jar file into the <plugins> dir on BASE - In the "install" file is said: "" 3. Log in to BASE as an administrator and run the plug-in auto-installation wizard by going to Administrate -> Plugins -> Definitions and click on the 'New' button. "" 4. Select the 'Automatically' option. - But I do not have the 'Automatically' option when creating 'New". Instead i have: "Name New plugin "Class "Path "Max memory (Use KB, MB or GB to specify units) "Trusted no yes "Allow immediate exection no yes auto What's wrong? Why that can't be done as listed in "Install" file? I recently apgraded to version 2.11.0. Maybe a BASE 2 version problem? __SECOND QUESTION: R/G quantile normalization Jari said: >Obviously R-G quantile is not supported since the methods in >net.sf.basedb.normalizers only work on ratios. - i am not expert on java developping.. but what does mean: methods in net.sf.basedb.normalizers only work on ratios - Do you mean it is not possible to implement plugins to perform R/G quantile normalizations? - how could i pass through this problem? __3RD QUESTION: Calculate ratios between sames chanels of 2 assays Since, for each assay i have a pool of RNA labelled with Cy5(as control for normalization between arrays), and conditions treatments labelled with cy3, can i create an new column expression which calculates ratio of ch(1)assay1/ch(1)assay2, and an other one for ch(2)? Thanks for your answers Yannick -- ---------------------------------------------------------- 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 ---------------------------------------------------------- ----------------------------------------------------- > Message: 3 > Date: Tue, 21 Apr 2009 09:55:07 +0200 > From: Jari H?kkinen <j...@thep.lu.se> > Subject: Re: [base] normalization and ratios between 2 bioassays > To: BASE ML <basedb-users@lists.sourceforge.net> > Message-ID: <49ed7bdb.5040...@thep.lu.se> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > 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/Universit? P. Sabatier >> P?le de Biotechnologies V?g?tales >> 24, chemin de Borde Rouge B.P. 17 Auzeville >> 31 326 CASTANET-TOLOSAN FRANCE >> ---------------------------------------------------------- >> ------------------------------------------------------------------------------ Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensign option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ 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
