I am trying to colour a limma generated MA plot by fold change. I can do it this way: status <- bugs.colour(RG,1) attr(status,"values") <- c("nonsignificant", "present", "absent", "Blank", "Buffer", "ACTB", "GAPDH", "Positive") attr(status,"col") <- c("black", "red", "green", "black", "brown", "pink", "yellow", "orange", "grey") plotMA(RG, array=1, status=status) bugs.colour <- function(RG, array) { status <- RG$genes$Status for (i in 1:length(status)) { if (status[i] == "gene") { if is.na(RG$other$LogRatio[i,array])) { status[i] = "nonsignificant" } else if (RG$other$LogRatio[i,array] > 0) { status[i] = "present" } else { status[i] = "absent" } } } status } but this seems to be a bit of a hack has i have hijacked the control status... my question is, is there a better more efficient way to do this? thanks adam

Hi Adam, Efficiency: have a look at the "ifelse" function for vectorised if-functionality that allows you to avoid the for-loop in your 'bugs.colour' function. Goodness: I don't think you need to be worrying about hijacking the control status for your purpose, since it's the limma::plotMA function that hijacked plot's "col" argument in the first place. However, if this leads to serious trouble, the cleanest is probably to write your own function on top of graphics::plot (or lattice::xyplot), since the added functionality of limma::plotMA is not that complex. Best wishes Wolfgang adam_pgsql scripsit 12/04/10 16:19: > I am trying to colour a limma generated MA plot by fold change. I can do it this way: > > status <- bugs.colour(RG,1) > attr(status,"values") <- c("nonsignificant", "present", "absent", "Blank", "Buffer", "ACTB", "GAPDH", "Positive") > attr(status,"col") <- c("black", "red", "green", "black", "brown", "pink", "yellow", "orange", "grey") > plotMA(RG, array=1, status=status) > > bugs.colour <- function(RG, array) { > status <- RG$genes$Status > > for (i in 1:length(status)) { > if (status[i] == "gene") { > if is.na(RG$other$LogRatio[i,array])) { > status[i] = "nonsignificant" > } > else if (RG$other$LogRatio[i,array] > 0) { > status[i] = "present" > } > else { status[i] = "absent" } > } > } > status > } > > but this seems to be a bit of a hack has i have hijacked the control status... my question is, is there a better more efficient way to do this? > > thanks > > adam > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber