Hi User, I am trying to plot my M-A levels using different colors for the controls. For that I created a spottype file, which looks like that: SpotType ControlType Color gene 0 black NC -1 green PC 1 red In my agilent files I don't have columns named "ID" or "Name", But I can sperate my controls with the ControlType column. This I also read in the the read.maimages() annotations. This is how I run the analysis (agilent two-color arrays) >targets <- readTargets("targets.txt") >SpotTypes = readSpotTypes() > RG <- read.maimages(targets, path="rawData", columns = list(G = "gMedianSignal", Gb = "gBGMedianSignal", R = "rMedianSignal", Rb = "rBGMedianSignal"), names = targets$Cy5, annotation = c("Row", "Col","FeatureNum", "ControlType","ProbeName", "GeneName") ) RG$gene$Status = controlStatus(SpotTypes, RG) to check the results of that I did: > table(RG$gene$Status) gene NC PC 43096 555 1563 But even than I don't see any controls in my plot. Everything is black. Do I do anything wrong? Is there another way to color different groups? Thanks Assa [[alternative HTML version deleted]]

Hi everyone, I try to add many vectors (L1,L2,L3....) to multiple list objects (a.list, b.list....) in a workspace. Somethings like below, but it is not working. Any suggestions will be appreciated. Best, John lf=ls(pattern=".lst")  for (x in listfiles) {     dat=read.delim(x,header=F)     for (i in lf) {     assign(i$add,as.numeric(dat[,3]))   #or i$add=as.numeric(dat[,3]     names(i)[names(i)=="add"]=substr(x,1,5)     print (i[1:3,])  }} ________________________________ From: Assa Yeroslaviz <frymor@gmail.com> To: bioconductor <bioconductor@stat.math.ethz.ch> Sent: Wednesday, August 1, 2012 9:29 AM Subject: [BioC] limma spottype Hi User, I am trying to plot my M-A levels using different colors for the controls. For that I created a spottype file, which looks like that: SpotType    ControlType    Color gene    0    black NC    -1    green PC    1    red In my agilent files I don't have columns named "ID" or "Name", But I can sperate my controls with the ControlType column. This I also read in the the read.maimages() annotations. This is how I run the analysis (agilent two-color arrays) >targets <- readTargets("targets.txt") >SpotTypes = readSpotTypes() > RG <- read.maimages(targets, path="rawData", columns = list(G = "gMedianSignal", Gb = "gBGMedianSignal", R = "rMedianSignal",   Rb = "rBGMedianSignal"), names = targets$Cy5, annotation = c("Row", "Col","FeatureNum", "ControlType","ProbeName", "GeneName") ) RG$gene$Status = controlStatus(SpotTypes, RG) to check the results of that I did: > table(RG$gene$Status) gene    NC    PC 43096  555  1563 But even than I don't see any controls in my plot. Everything is black. Do I do anything wrong? Is there another way to color different groups? Thanks Assa     [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]

Hi Assa, On 8/1/2012 9:29 AM, Assa Yeroslaviz wrote: > Hi User, > > I am trying to plot my M-A levels using different colors for the controls. > For that I created a spottype file, which looks like that: > SpotType ControlType Color > gene 0 black > NC -1 green > PC 1 red > > In my agilent files I don't have columns named "ID" or "Name", But I can > sperate my controls with the ControlType column. This I also read in the > the read.maimages() annotations. > > This is how I run the analysis (agilent two-color arrays) > >> targets<- readTargets("targets.txt") >> SpotTypes = readSpotTypes() >> RG<- read.maimages(targets, path="rawData", columns = list(G = > "gMedianSignal", Gb = "gBGMedianSignal", R = "rMedianSignal", > Rb = "rBGMedianSignal"), names = targets$Cy5, annotation = c("Row", > "Col","FeatureNum", "ControlType","ProbeName", "GeneName") ) > RG$gene$Status = controlStatus(SpotTypes, RG) > to check the results of that I did: >> table(RG$gene$Status) I believe you want RG$genes$Status. Best, Jim > gene NC PC > 43096 555 1563 > > But even than I don't see any controls in my plot. Everything is black. > Do I do anything wrong? > > Is there another way to color different groups? > > Thanks > Assa > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099