hits=-0.6 tests=BAYES_00,TVD_SPACED_SUBJECT_WORD X-USF-Spam-Flag: NO NO Hi all, I'm relatively new to Bioconductor and am still figuring out how to use MiPP for my work. >From the help sheet in the MiPP documentation, ########## #Example 1: When an independent test set is available data(leukemia) #Normalize combined data leukemia <- cbind(leuk1, leuk2) leukemia <- mipp.preproc(leukemia, data.type="MAS4") #Train set x.train <- leukemia[,1:38] y.train <- factor(c(rep("ALL",27),rep("AML",11))) #Test set x.test <- leukemia[,39:72] y.test <- factor(c(rep("ALL",20),rep("AML",14))) #Compute MiPP out <- mipp(x=x.train, y=y.train, x.test=x.test, y.test=y.test, probe.ID = 1:nrow(x.train), n.fold=5, percent.cut=0.05, rule="lda") #Print candidate models out$model Order Gene Tr.ER Tr.MiPP Tr.sMiPP Te.ER Te.MiPP Te.sMiPP Select 1 1 571 0.0526 30.86 0.8122 0.1176 23.92 0.7035 2 2 436 0.0000 36.89 0.9707 0.0294 30.41 0.8945 3 3 366 0.0000 37.95 0.9988 0.0294 31.35 0.9222 4 4 457 0.0000 38.00 0.9999 0.0294 32.14 0.9453 5 5 413 0.0000 38.00 1.0000 0.0294 32.18 0.9464 6 6 635 0.0000 38.00 1.0000 0.0000 33.75 0.9927 ** 7 7 648 0.0000 38.00 1.0000 0.0000 33.62 0.9889 8 8 181 0.0000 38.00 1.0000 0.0294 31.99 0.9409 9 9 309 0.0000 38.00 1.0000 0.0000 33.46 0.9842 10 10 99 0.0000 38.00 1.0000 0.0882 28.56 0.8400 Here are some questions, i) how do I elucidate the misclassified samples in the model? ie which samples in the training or testing set were false positive/false negative? ii) The most parsimonious model is 6 with genes 571,436,366,457,413 and 635. Is it possible to elucidate the misclassified samples in previous orders, eg order 1 with Te.Error Rate of 0.1176? iii) Could i use the built model to validate on other independent datasets? thank you regards Julian Lee Bioinformatics Specialist National Cancer Center Singapore R version 2.5.1 (2007-06-27) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" other attached packages: MiPP MASS e1071 class Biobase "1.8.0" "7.2-34" "1.5-16" "7.2-34" "1.14.1"

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