Hi, I think this is a problem with negative and zero intensity values (due to FG-BG). You need to decide how to treat these intensities and the filter or modify these numbers. After resolving this, you can proceed as you describe.
Cheers, Jari Ana Conesa wrote: > Hi > > I am using BASE to store and analyze 2 color (GenePix) data from a > costum cDNA array. > I am addressing now the analysis of an experiment. I created a raw bioassay > out of raw data files and I would like now to normalize. I am not sure > which is the standard procedure to do this. At first I calculated FG-BG > using the formula intensity calculator and then I tried to compute M > values on the result as log2(ch1/ch2) with the idea of running lowess > normalization on this result, but this is giving me a "value" error, so > I guess this is not the way. Could anyone give me a bit of help on this > Thanks a lot > Ana > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2005. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] > -- Jari Hakkinen, PhD Complex Systems Division mailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46 2229347 Lund University fax: +46 (0)46 2229686 Solvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
