Dear Simon, Thank you very much for your help! Now I solved the problem following your advice. After I loaded "genefilter",the function "rowSds" run. At last I got the results.But there are some other little problems and I wonder why they happened. 1/ > sum.sam.out<-summary(sam.out,30,ll=FALSE); Error in .local(object, ...) : unused arguments in argument((ll = FALSE)) The error message above appears in R 2.9 but not in R 2.4 2/ > library(estrogen); Error in library(estrogen) : Packages not available:'estrogen' The error message above appears in all version of R. "estrogen" is the package found in my reference book. This step is optional,so I slip it. 3/ > heatmap(exprs(AffyExpData)[sel,],col=gentlecol(256)); Error in image.default(1:nc, 1:nr, x, xlim = 0.5 + c(0, nc), ylim = 0.5 + :function not available:"gentlecol" The error message above appears in all version of R. "gentlecol" is also the function found in my reference book. I replace it by below: > heatmap(exprs(AffyExpData)[sel,],col =rainbow(256)); or > heatmap(exprs(AffyExpData)[sel,],col = cm.colors(256)); It runs. But I wonder that is there many errors in my book? Whether 'estrogen' and "gentlecol" are very old and have been removed now or did not exist at all? Yours hopefully, 2009-05-17 wangchuanming [[alternative HTML version deleted]]

"wangchuanming" <wangchuanming at="" 126.com=""> writes: > Dear Simon, > > Thank you very much for your help! > > Now I solved the problem following your advice. After I loaded "genefilter",the function "rowSds" run. At last I got the results.But there are some other little problems and I wonder why they happened. > > 1/ >> sum.sam.out<-summary(sam.out,30,ll=FALSE); > Error in .local(object, ...) : unused arguments in argument((ll = FALSE)) > > The error message above appears in R 2.9 but not in R 2.4 your 'sam.out' instance is a class of object "SAM". To see this, try > class(sam.out) To see what functions are available on this object, try > ?"SAM-class" and > help.sam(summary) In this particular case, I believe that 'll' refered to LocusLink information, and this is not so useful these days; since you were invoking summary with ll=FALSE, there would seem to be little harm in just omitting it. > 2/ >> library(estrogen); > Error in library(estrogen) : Packages not available:'estrogen' > > The error message above appears in all version of R. "estrogen" is > the package found in my reference book. This step is optional,so I > slip it. Bioconductor has a number of 'experimental data' packages available. Likely elsewhere in your book there is the command (or one that accomplishes the same thing) source('http://bioconductor.org/biocLite.R') biocLite('estrogen') this installs the 'estrogen' package, so that it is available in subsequent sessions. You will then be able to evaluate library('estrogen') in any session where you want to access this data. > 3/ >> heatmap(exprs(AffyExpData)[sel,],col=gentlecol(256)); > Error in image.default(1:nc, 1:nr, x, xlim = 0.5 + c(0, nc), ylim = 0.5 + :function not available:"gentlecol" > > > The error message above appears in all version of R. "gentlecol" is > also the function found in my reference book. I replace it by below: > >> heatmap(exprs(AffyExpData)[sel,],col =rainbow(256)); > or >> heatmap(exprs(AffyExpData)[sel,],col = cm.colors(256)); > > It runs. But I wonder that is there many errors in my book? Whether > 'estrogen' and "gentlecol" are very old and have been removed now or > did not exist at all? gentlecol is defined in the estrogen package, so it should be available once you have estrogen loaded. Martin > > Yours hopefully, > > > 2009-05-17 > > > > wangchuanming > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793

Thank you very much! 2009-05-29 wangchuanming [[alternative HTML version deleted]]