expr.matrix is a matrix and it did work when I inverted the syntax. Many thanks Daniel Martin Morgan wrote: > Hi Daniel, > > I think the basic syntax is inverted -- > > rownames(obj)[1:3] <- 3:1 > > instead of > > rownames(obj[1:3,]) <- 3:1 > > It's a little hard to tell what expr.matrix is. A matrix? > >> m <- matrix(0,10,5) >> rownames(m)[1:4] <- 4:1 # need to have dims before they can be changed! > Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent >> rownames(m) <- 1:10 >> rownames(m)[1:4] <- 4:1 >> m > [,1] [,2] [,3] [,4] [,5] > 4 0 0 0 0 0 > 3 0 0 0 0 0 > 2 0 0 0 0 0 > 1 0 0 0 0 0 > 5 0 0 0 0 0 > 6 0 0 0 0 0 > 7 0 0 0 0 0 > 8 0 0 0 0 0 > 9 0 0 0 0 0 > 10 0 0 0 0 0 > > > But maybe it's an 'ExpressionSet' or 'exprSet'. What does > >> class(expr.matrix) > > say? If it's an ExpressionSet (or I think also an exprSet), then > you'll want to do the equivalent of > >> obj <- new("ExpressionSet", exprs=matrix(0,10,5)) >> obj > ExpressionSet (storageMode: lockedEnvironment) > assayData: 10 features, 5 samples > element names: exprs > phenoData > sampleNames: 1, 2, ..., 5 (5 total) > varLabels and varMetadata: none > featureData > featureNames: 1, 2, ..., 10 (10 total) > varLabels and varMetadata: none > experimentData: use 'experimentData(object)' > Annotation character(0) >> featureNames(obj) > [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" >> featureNames(obj)[2:4] <- 4:2 >> featureNames(obj) > [1] "1" "4" "3" "2" "5" "6" "7" "8" "9" "10" >> obj > ExpressionSet (storageMode: lockedEnvironment) > assayData: 10 features, 5 samples > element names: exprs > phenoData > sampleNames: 1, 2, ..., 5 (5 total) > varLabels and varMetadata: none > featureData > featureNames: 1, 4, ..., 10 (10 total) > varLabels and varMetadata: none > experimentData: use 'experimentData(object)' > Annotation character(0) > > Hope that helps, > > Martin > > > Daniel Brewer <daniel.brewer at="" icr.ac.uk=""> writes: > >> Hi, >> >> I have a expression dataset where I want to join Affymetrix U133A and B >> arrays. The rownames of the expression matrix are set to the probe >> names. To do this I want to treat all the probe names that are shared >> between the arrays as unique by appending an "_A" or "_B". I do this by >> finding the names of the probe that are shared and then running: >> >> rownames(expr.matrix[match(ProbeIntersect,rownames(expr.matrix)),]) <- >> paste(rownames(expr.matrix[match(ProbeIntersect,rownames(expr.matri x)),]),"_A",sep="") >> >> Where "expr.matrix" is the expression matrix and "ProbeIntersect" is the >> list of probe names that are shared. This command though does not seem >> to change the row names. Any idea what I am doing wrong? >> >> Thanks >> >> Daniel >> -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Email: daniel.brewer at icr.ac.uk ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addre...{{dropped}}