Dear All, It looks like I found a bug in the function pamr.plotcen() of the package pamr in this row: genenames <- data$genenames[fit$gene.subset] there is no such name in the output list of pamr.train(mydata) Thanks Alex > set.seed(120) > x <- matrix(rnorm(1000*20),ncol=20) > y <- sample(c(1:4),size=20,replace=TRUE) > mydata <- list(x=x,y=y) > mytrain <- pamr.train(mydata) 123456789101112131415161718192021222324252627282930> mycv <- pamr.cv(mytrain, mydata) 1234Fold 1 :123456789101112131415161718192021222324252627282930 Fold 2 :123456789101112131415161718192021222324252627282930 Fold 3 :123456789101112131415161718192021222324252627282930 Fold 4 :123456789101112131415161718192021222324252627282930 > pamr.plotcv(mycv) > pamr.plotcen(mytrain, mydata,threshold=1.6) Error in text.default(rep(0, nd), seq(nd), label = g, cex = 0.4, adj = 0, : zero length 'labels' >names(mytrain) [1] "y" "proby" "yhat" [4] "prob" "centroids" "centroid.overall" [7] "sd" "threshold" "nonzero" [10] "threshold.scale" "se.scale" "scale.sd" [13] "call" "hetero" "norm.cent" [16] "prior" "offset" "sign.contrast" [19] "errors" "gene.subset" "sample.subset" [22] "ngroup.survival" "problem.type" > sessionInfo() R version 2.12.2 (2011-02-25) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] pamr_1.51 survival_2.36-5 cluster_1.13.3 xtable_1.5-6 [5] Rmagpie_1.6.0 Biobase_2.10.0 RWeka_0.4-7 loaded via a namespace (and not attached): [1] class_7.3-3 e1071_1.5-25 grid_2.12.2 kernlab_0.9-12 [5] rJava_0.8-8 RWekajars_3.7.3-1 [[alternative HTML version deleted]]

Hi Alex -- Thanks for the report and reproducible example; see the comment below... On 06/06/2011 11:33 AM, Alogmail2 at aol.com wrote: > > Dear All, > > It looks like I found a bug in the function pamr.plotcen() of the package > pamr > in this row: > > genenames<- data$genenames[fit$gene.subset] > > there is no such name in the output list of pamr.train(mydata) > > > Thanks > > Alex > > > > > > > > > >> set.seed(120) >> x<- matrix(rnorm(1000*20),ncol=20) >> y<- sample(c(1:4),size=20,replace=TRUE) >> mydata<- list(x=x,y=y) Try mydata <- list(x=x,y=y, genenames=as.character(1:1000)) I arrived at this by looking at ?pamr.plotcen and knowing that the examples have to work for the package to be available for biocLite. Martin >> mytrain<- pamr.train(mydata) > 123456789101112131415161718192021222324252627282930> mycv<- > pamr.cv(mytrain, mydata) > 1234Fold 1 :123456789101112131415161718192021222324252627282930 > Fold 2 :123456789101112131415161718192021222324252627282930 > Fold 3 :123456789101112131415161718192021222324252627282930 > Fold 4 :123456789101112131415161718192021222324252627282930 >> pamr.plotcv(mycv) >> pamr.plotcen(mytrain, mydata,threshold=1.6) > Error in text.default(rep(0, nd), seq(nd), label = g, cex = 0.4, adj = 0, > : > zero length 'labels' > > >> names(mytrain) > [1] "y" "proby" "yhat" > [4] "prob" "centroids" "centroid.overall" > [7] "sd" "threshold" "nonzero" > [10] "threshold.scale" "se.scale" "scale.sd" > [13] "call" "hetero" "norm.cent" > [16] "prior" "offset" "sign.contrast" > [19] "errors" "gene.subset" "sample.subset" > [22] "ngroup.survival" "problem.type" > > > > > > > >> sessionInfo() > R version 2.12.2 (2011-02-25) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] pamr_1.51 survival_2.36-5 cluster_1.13.3 xtable_1.5-6 > [5] Rmagpie_1.6.0 Biobase_2.10.0 RWeka_0.4-7 > > loaded via a namespace (and not attached): > [1] class_7.3-3 e1071_1.5-25 grid_2.12.2 kernlab_0.9-12 > > [5] rJava_0.8-8 RWekajars_3.7.3-1 > > > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793