Thanx a lot for your prompt answer F?tima _______ 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 > -----Original Message----- > From: Ramon Diaz-Uriarte [mailto:rdiaz@cnio.es] > Sent: 02 July 2003 13:50 > To: F?tima N??ez; bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] Help with "Error in Summary.factor(..., na.rm = na.rm) > : "max" not meaningful for factors", please? > > 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 >