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

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