Hi all, I am trying to take data from a scanner that is not part of the "core" group supported by limma, and create an RGList object from it, using the minimal components as defined in the limma docs. I've read in the CSV file and isolated the green and red F/G and B/G data for each chip, but what is unclear in the docs is the format that they need to be in... In other words, is the order of slots/list components in the RGList object R1, G1, Rb1, Gb1...R1n, G1n, Rbn, Gbn for each chip, or is it R1...Rn, G1...Gn, Rb1...Rn, Gb1...Gbn (where n is the number of chips)? Thanks in advance, Ken

The Limma class "RGList" is a list with elements; > names(RG) [1] "R" "G" "Rb" "Gb" "weights" "targets" "genes" "printer" R - p x n matrix of red foreground intensities (p spots/genes, n slides) G - p x n matrix of red foreground intensities Rb - p x n matrix of red background intensities Gb - p x n matrix of red background intensities weights - optional p x n matrix of spot weights targets - auxillary cy3/cy5 mapping and/or filenames genes - p x 5 matrix of gal mappings (usually) printer - list of grid/spot row/column layout You can construct one like this; library(limma) RG <- new("RGList") RG$weights <- matrix(...) # Appropriate matrix of spot flags/weights RG$targets <- readTargets(...) # targets from tab delimited text file RG$genes <- readGAL(...) # GAL text file information or from matrix(...) RG$printer <- getLayout(RG$genes) RG$R <- matrix(...) # Repeat for G,Rb,Rg You can add other auxilary information you think appropriate into the list. Other option is to modify read.maimages(...) to work for your input files. Marcus >>> "Ken Termiso" <jerk_alert at="" hotmail.com=""> 20/06/2005 9:19:09 p.m. >>> Hi all, I am trying to take data from a scanner that is not part of the "core" group supported by limma, and create an RGList object from it, using the minimal components as defined in the limma docs. I've read in the CSV file and isolated the green and red F/G and B/G data for each chip, but what is unclear in the docs is the format that they need to be in... In other words, is the order of slots/list components in the RGList object R1, G1, Rb1, Gb1...R1n, G1n, Rbn, Gbn for each chip, or is it R1...Rn, G1...Gn, Rb1...Rn, Gb1...Gbn (where n is the number of chips)? Thanks in advance, Ken _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ______________________________________________________ The contents of this e-mail are privileged and/or confidenti...{{dropped}}