hi, I have a control column : "ctl" in gal file with control information, and I define maLayout like this : manip.layout <- read.marrayLayout(fname=file.gal,ngr=ngr,ngc=ngc,nsr=nsr,nsc=nsc,skip= skip, ctl.col = "ctl") x <- as.character(maInfo(manip.gnames)[,"ctl"]) y <- rep("probes", maNspots(manip.layout)) y[x == "control"] <- "control" slot(manip.layout, "maControls") <- as.factor(y) By this way, fonction maQualityPlots from the marrayQuality package creates DotPlots with control spots (in green) but not with empty spots. How and where empty spots are they defined in the marray format ? thanks

Hi, I have a programming problem that I have ran into once or twice before Using the command ls returns the names of the files in the active R environment. I need to use the data contained in these files but ls() only returns the names of the files. I'm wondering if there is a function that can be used to access the data? An example of the problem is as follows. > ag<-1:10 > bu<-c('h','e','l','p') > Ci<-ag > length(ag) [1] 10 > length(ls()[1]) [1] 1 > ls()[1] [1] "ag" The length of ag is 10 but the length of its name is 1. How do I get the length command to look at the data instead of the name? Thanks Ian

Hi, marray is using a reference table named controlCode to check the control status of the spotted probes. controlCode is a matrix with 2 columns named: Pattern and Name. You can check the default controlCode by typing in R: library(marray) controlCode Pattern Name 1 "Buffer" "Buffer" 2 "Empty" "Empty" 3 "EMPTY" "Empty" 4 "AT" "Negative" 5 "NC" "Negative" 6 "M200009348" "Positive" 7 "M200012700" "Positive" 8 To specify your own controls, you have to create your own controlCode matrix. This can be done by either using the readcontrolCode function in marray or by reading a tab-delimited text file directly. controlCode <- as.matrix(read.table("mycontrolCode.txt", sep="\t",header=TRUE, quote="\"", fill=TRUE))) Then, you can fill up the maControls slot by calling the function maGenControls. It is easier to use read.Galfile instead of read.marrayLayout and read.marrayInfo to read your array information. You will need to add your control column name in the info.id argument: Assume mraw is a marrayRaw object: test <- read.Galfileinfo.id = c("ID", "Name", "ctl")) maLayout(mraw) <- test$layout maGnames(mraw) <- test$gnames Then, you can define your controls using the function maGenControls, specifying your control column in the id argument: maControls(mraw) <- maGenControls(Gnames, controlcode=newControlCode, id = "correctCtlID") Regards, Agnes -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Ghislaine Guigon Sent: Tuesday, March 01, 2005 4:46 AM To: bioconductor@stat.math.ethz.ch Subject: [BioC] marrayQuality & marray : empty ? hi, I have a control column : "ctl" in gal file with control information, and I define maLayout like this : manip.layout <- read.marrayLayout(fname=file.gal,ngr=ngr,ngc=ngc,nsr=nsr,nsc=nsc,skip= sk ip, ctl.col = "ctl") x <- as.character(maInfo(manip.gnames)[,"ctl"]) y <- rep("probes", maNspots(manip.layout)) y[x == "control"] <- "control" slot(manip.layout, "maControls") <- as.factor(y) By this way, fonction maQualityPlots from the marrayQuality package creates DotPlots with control spots (in green) but not with empty spots. How and where empty spots are they defined in the marray format ? thanks _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor