[BioC] limma spottype
James W. MacDonald
jmacdon at uw.edu
Wed Aug 1 15:39:46 CEST 2012
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$Status = controlStatus(SpotTypes, RG)
> to check the results of that I did:
I believe you want RG$genes$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?
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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