Thanks for the hint. I rewrote the program Here is how it looks like when apply to AffyBatch which contain a phenoData vector "population" describing the data structure. The thing I can't managed to do without going through a matrix to stock the expression data, is to have the name of the corresponding experiment below each boxplot (i.e for the moment I have the default numbering). the first version of the script (see bottom) is doing that not this new one. This one is creating a legend inside the graph. ## # usage: myboxplot("1234_at", abatch) myboxplot <- function(id,abatch){ require(mgu74av2) require(gplots) require(RColorBrewer) # Grab title y <- mget (id, env= mgu74av2GENENAME) names(y) <- NULL # Colors colors <- brewer.pal(9, "Set1") boxplot(exprs(abatch)[rownames(exprs(abatch))==id] ~ abatch$population, col=colors) title(main=y, sub=id) smartlegend(x="left",y="top", inset=0, c("1: Exp1", "2: Exp2", "3: Exp3", "4: Exp4", "5: Exp5", "6: Exp6"), fill=colors) } #end On Jan 9, 2006, at 15:49, James W. MacDonald wrote: > David Ruau wrote: >> -----BEGIN PGP SIGNED MESSAGE----- >> Hash: SHA1 >> Hi, >> I wrote a little function to do a boxplot for a row element of a >> numeric matrix. Indeed for a specific probeset of a expression value >> matrix but the problem is not with bioconductor functions but on the >> right use of R. >> Is there a simpler way to do a boxplot for a specific probeset from >> either a AffyBatch or an expression matrix? >> - ---- code ---- >> myboxplot <- function(id,e.mat){ >> require(mgu74av2) >> # grab the expression values >> x <- e.mat[rownames(e.mat)==id] >> # make column of those expression value >> c1 <- as.list(t(x[1:3])) # Exp1 >> c2 <- as.list(t(x[4:6])) # Exp2 >> c3 <- as.list(t(x[7:9])) # Exp3 >> c4 <- as.list(t(x[10:12])) # Exp4 >> c5 <- as.list(t(x[13:14])) # Exp5 >> c6 <- as.list(t(x[15:17])) # Exp6 >> # Little transformation for c5 as there is only 2 value for it and 3 >> for the others. >> c5 <- c(c5, NA) # because only 2 values >> >> # combinaison of the column >> x <- cbind(c1,c2,c3,c4,c5,c6) >> >> # Convert to a dataframe >> x <- as.data.frame(x) >> # Add name to the column >> colnames(x) <- c("Exp1", "Exp2", "Exp3", "Exp4", "Exp5", "Exp6") >> >> # Grab gene name for plot's title >> y <- mget (id, env= mgu74av2GENENAME) >> names(y) <- NULL >> boxplot(x) >> title(main=y, sub=id) >> } > > That is a lot of work to get a boxplot. You should be able to get the > same thing with much less work. > > y <- get(id, mgu74av2GENENAME) > expt <- as.factor(rep(1:6, each=3)[-13]) > boxplot(exprs(e.mat)[id,]~expt, main = y, sub = id, names = > paste("Exp", 1:6, sep="")) >> - ---- >> Thanks, >> David >> -----BEGIN PGP SIGNATURE----- >> Version: GnuPG v1.4.1 (Darwin) >> iD8DBQFDwmHB7EoGVUIQyhERAuRiAJ491zrSB/zD7P8aRMkc7nKPu496rwCggnsi >> gi2RwP7t2CQcC0pTsTVFsos= >> =6H0E >> -----END PGP SIGNATURE----- >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > > -- > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623