Hi all, I am a new user for S-PLUS as well as this group, I have a problem in Li Wong method, please help me to getout from the warnings > LiWong <- express(affydb, bg=subtractmm, normalize=F, summary.stat=li.wong) Background correcting Preparing Data Computing expression. This may take a while. There were 50 warnings (use warnings() to see them) > warnings() Warning messages -- 1: No convergence in inner loop after 50 in outerler tieration 4 in: fit.li.wong(t(data.matrix), remove.outliers, normal.array.quantile, ... 2: No convergence achieved in outlier loop in: fit.li.wong(t(data.matrix), remove.outliers, normal.array.quantile, ... 3: No convergence achieved in outlier loop in: fit.li.wong(t(data.matrix), remove.outliers, normal.array.quantile, ... ### #lots... ### #Everytime in LiWong method geting lots of warnings, my #version of S-PLUS > version S-PLUS Analytic Server 2.1 Release 2 for Sun SPARC, SunOS 5.6 : 2002 Thanks, any feedback is appreciated, Burri ===== Raghunadha Reddy Burri Interdisciplinary Centre for Bioinformatics (IZBI) Lehrstuhl f?r Bioinformatik Institut f?r Informatik Universit?t Leipzig Kreuzstrasse 7b D-04103 Leipzig E-Mail: burri@izbi.uni-leipzig.de __________________________________________________________________ Logos und Klingelt?ne f?rs Handy bei http://sms.yahoo.de

the li and wong algoritm (as described in the PNAS paper) doesnt always converge. in your case for 50 probes. This is more common when you have few arrays. On Fri, 16 May 2003, Raghu burri wrote: > Hi all, > > I am a new user for S-PLUS as well as this group, I > have a problem in Li Wong method, please help me to > getout from the warnings > > > LiWong <- express(affydb, bg=subtractmm, > normalize=F, summary.stat=li.wong) > Background correcting > Preparing Data > Computing expression. This may take a while. > There were 50 warnings (use warnings() to see them) > > > warnings() > Warning messages -- > 1: No convergence in inner loop after 50 in outerler > tieration 4 > in: fit.li.wong(t(data.matrix), remove.outliers, > normal.array.quantile, > ... > 2: No convergence achieved in outlier loop > in: fit.li.wong(t(data.matrix), remove.outliers, > normal.array.quantile, > ... > 3: No convergence achieved in outlier loop > in: fit.li.wong(t(data.matrix), remove.outliers, > normal.array.quantile, > ... > ### > #lots... > ### > #Everytime in LiWong method geting lots of warnings, > my #version of S-PLUS > > > version > S-PLUS Analytic Server 2.1 Release 2 for Sun SPARC, > SunOS 5.6 : 2002 > > Thanks, any feedback is appreciated, > > Burri > > ===== > Raghunadha Reddy Burri > Interdisciplinary Centre for Bioinformatics (IZBI) > Lehrstuhl f?r Bioinformatik Institut f?r Informatik > Universit?t Leipzig > Kreuzstrasse 7b > D-04103 Leipzig > E-Mail: burri@izbi.uni-leipzig.de > > __________________________________________________________________ > > > Logos und Klingelt?ne f?rs Handy bei http://sms.yahoo.de > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >