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]]