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Try modfying your statement x[,"FlagA"]="A"|"B"|"C" etc to use the test operator rather than the assignment operator. Something like; okred <- x[,"FlagA"]=="A" | x[,"FlagA"]=="B" | x[,"FlagA"]=="C" Marcus On 12/1/06 8:52 AM, "Yolande Tra" <yvtsma at="" rit.edu=""> wrote: > Hi, > > I have cDNA array data processed through TIGR Spotfinder. I tried the > followimg for Spot quality weigth but it did not work > > myfun <- function(x) { > + okred <- x[,"FlagA"]="A"|"B"|"C" > + okgreen <- x[,"FlagB"]="A"|"B"|"C" > + as.numeric(okgreen & okred)} >> RG <- read.maimages(filenames, wt.fun=myfun) > Error in read.maimages(filenames, wt.fun = myfun) : > must specify columns for generic input > > The Flags for each channel 1 and 2 are nonnumerical values A, B or C if good > spots. They are in columns named Flag A and Flag B in each of 11 files defined > below > >> filenames > [1] "IE1107_bottomGrid.mev" "IE1107_topGrid.mev" "IE1108_bottomGrid.mev" > [4] "IE1109_bottomGrid.mev" "IE1109_topGrid.mev" "IE1110_bottomGrid.mev" > [7] "IE1111_topGrid.mev" "IE1113_bottomGrid.mev" "IE1113_topGrid.mev" > [10] "IE2637_bottomGrid.mev" "IE2637_topGrid.mev" > > Can anyone please help me out? Thanks. > > Yolande > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 ______________________________________________________ The contents of this e-mail are privileged and/or confidenti...{{dropped}}