I am trying to transform the vector (pm and mm) extracted from @exprs to a matrix (2-D layout), so an image can be plotted. It works out. Now, when I back-transform the image matrix to the vector, there are some trouble. See the code below. Seems that the matrix has to be transposed somehow. Any ideas? Thanks! -Simon library (affy) data (affybatch.example) # has 3 chips x<- affybatch.example m.vector <- log2( x at exprs[, 2]) # take the second array x.pos <- (1:nrow(x)) - (1 + getOption("BioC")$affy$xy.offset) y.pos <- (1:ncol(x)) - (1 + getOption("BioC")$affy$xy.offset) # from vector to matrix m <- as.matrix(rev(as.data.frame(matrix(m.vector, nrow = length(x.pos), ncol = length(y.pos))))) # ???????????????? # from matrix to vector m0.vector<- as.vector (m) # this does not work, need some massage of m # see if it works sum (m.vector!= m0.vector)

On Jan 31, 2006, at 4:34 PM, Simon Lin wrote: > I am trying to transform the vector (pm and mm) extracted from > @exprs to a > matrix (2-D layout), so an image can be plotted. It works out. Yes. I assume the code given below has been snapped from getMethod("image", "AffyBatch")\ (Why do you want to generate that code anyway, when suitable image functions exists?) > > > Now, when I back-transform the image matrix to the vector, there > are some > trouble. See the code below. > > > > Seems that the matrix has to be transposed somehow. Any ideas? > Thanks! -Simon > > > > library (affy) > > data (affybatch.example) # has 3 chips > > x<- affybatch.example > > m.vector <- log2( x at exprs[, 2]) # take the second array > > > > x.pos <- (1:nrow(x)) - (1 + getOption("BioC")$affy$xy.offset) > > y.pos <- (1:ncol(x)) - (1 + getOption("BioC")$affy$xy.offset) > > # from vector to matrix > > m <- as.matrix(rev(as.data.frame(matrix(m.vector, nrow = length > (x.pos), > > ncol = length(y.pos))))) If you debug this line, you will understand why a simple as.matrix does not work. Basically, first a matrix is created. It is then converted to a data.frame so that rev() works on columns. Look: > matrix(1:9, nrow = 3) [,1] [,2] [,3] [1,] 1 4 7 [2,] 2 5 8 [3,] 3 6 9 > as.data.frame(matrix(1:9, nrow = 3)) V1 V2 V3 1 1 4 7 2 2 5 8 3 3 6 9 > rev(as.data.frame(matrix(1:9, nrow = 3))) V3 V2 V1 1 7 4 1 2 8 5 2 3 9 6 3 > as.matrix(rev(as.data.frame(matrix(1:9, nrow = 3)))) V3 V2 V1 1 7 4 1 2 8 5 2 3 9 6 3 > as.vector(as.matrix(rev(as.data.frame(matrix(1:9, nrow = 3))))) [1] 7 8 9 4 5 6 1 2 3 Ok? /Kasper > > > # ???????????????? > > # from matrix to vector > > m0.vector<- as.vector (m) # this does not work, need some > massage of m > > # see if it works > > sum (m.vector!= m0.vector) > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor