Hello all, At the moment I'm trying to obtain adjusted p-values using the maxT and minP functions on my data as described below, but when I try to implement any of the two I obtain the error shown. I have looked the ?Summary.factor help but I have to admit I didn't quite understand it. Could anybody please help me with this error in order to know what I'm doing wrong? >rmadata2$Genotype [1] CONT CONT CONT VAV2 VAV2 VAV2 Levels: CONT VAV2 > Index1 <- which(rmadata2$Genotype=="CONT") > Index2 <- which(rmadata2$Genotype=="VAV2") > scores <- esApply (rmadata2, 1, function(x) { + tmp <-t.test(x[Index2], x[Index1], var.equal =TRUE) + c(mean(tmp$estimate), -diff(tmp$estimate), tmp$statistic, tmp$p.value) + }) > scores <- t(scores) > colnames(scores) <- c("a", "m", "t.test", "p.value") > sum(scores[, 4] <= 0.05) [1] 1130 > sum(scores[, 4] <= 0.01) [1] 318 > tmp <- mt.rawp2adjp(scores[,4]) > adj.p.values <- tmp$adjp[order(tmp$index), -1] > scores <- cbind(scores, adj.p.values) > tmp <- mt.maxT(exprs(rmadata2), rmadata2$Genotype) Error in Summary.factor(..., na.rm = na.rm) : "max" not meaningful for factors Thanks in advance for your help and sorry if this is not a relevant question for BioC, Fatima _______ ? ? F?tima N??ez, PhD Centre for Cancer Research (CIC) University of Salamanca-CSIC Campus Unamuno 37007 Salamanca?????????????????????????????????????????????????? Spain Phone: + 34 923 294802 Fax:?????+ 34 923 294743 E-mail: fnunez@usal.es

Hola F?tima, I think the problem is that your class labels (rmadata2$Genotype) are a factor, but they should be a vector of integers starting at 0. The help for mt.maxT says: "classlabel: A vector of integers corresponding to observation (column) class labels. For k classes, the labels must be integers between 0 and k-1." You can easily achieve that by doing: my.classlabels <- as.numeric(rmadata2$Genotype) - 1 Best, Ram?n On Wednesday 02 July 2003 13:27, F?tima N??ez wrote: > Hello all, > > At the moment I'm trying to obtain adjusted p-values using the maxT and > minP functions on my data as described below, but when I try to > implement any of the two I obtain the error shown. I have looked the > ?Summary.factor help but I have to admit I didn't quite understand it. > Could anybody please help me with this error in order to know what I'm > doing wrong? > > >rmadata2$Genotype > > [1] CONT CONT CONT VAV2 VAV2 VAV2 > Levels: CONT VAV2 > > > Index1 <- which(rmadata2$Genotype=="CONT") > > Index2 <- which(rmadata2$Genotype=="VAV2") > > scores <- esApply (rmadata2, 1, function(x) { > > + tmp <-t.test(x[Index2], x[Index1], var.equal =TRUE) > + c(mean(tmp$estimate), -diff(tmp$estimate), tmp$statistic, > tmp$p.value) > + }) > > > scores <- t(scores) > > colnames(scores) <- c("a", "m", "t.test", "p.value") > > sum(scores[, 4] <= 0.05) > > [1] 1130 > > > sum(scores[, 4] <= 0.01) > > [1] 318 > > > tmp <- mt.rawp2adjp(scores[,4]) > > adj.p.values <- tmp$adjp[order(tmp$index), -1] > > scores <- cbind(scores, adj.p.values) > > tmp <- mt.maxT(exprs(rmadata2), rmadata2$Genotype) > > Error in Summary.factor(..., na.rm = na.rm) : > "max" not meaningful for factors > > Thanks in advance for your help and sorry if this is not a relevant > question for BioC, > Fatima > > _______ > > > > F?tima N??ez, PhD > Centre for Cancer Research (CIC) > University of Salamanca-CSIC > Campus Unamuno > 37007 Salamanca > Spain > Phone: + 34 923 294802 > Fax: + 34 923 294743 > E-mail: fnunez@usal.es > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Ram?n D?az-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://bioinfo.cnio.es/~rdiaz